Problem in calculating VdW Energy

Hi,

I use Materials Studio and LAMMPS simultaneously for a polyimide.

The problem i have is that, while MS Forcite module calculates my structure’s VdW energy as -78.516, in LAMMPS i have -88.7126.

I have checked my pair parameters for so many times and there are no problems in them.

I use pcff as force-field and my input file looks like;

clear

units real
boundary p p p
atom_style full

pair_style lj/class2/coul/long 15
kspace_style ewald 1.0e-004
special_bonds lj 0.0 0.0 1.0 coul 0.0 0.0 1.0

bond_style class2
angle_style class2
dihedral_style class2
improper_style class2

neighbor 2.0 bin
neigh_modify every 1 delay 2 check yes page 100000000 one 100000

read_data stablyapi.lammps05
#read_restart TR-m-p.restart.3000000

velocity all create 308.0 4928459 rot yes dist gaussian

#FIX
thermo_style multi
thermo 10000

#DUMP

dump 1 all custom 100000 6fdadam760.lammpstrj id type xs ys zs ix iy iz

restart 100000 stblypn.restart

timestep 1
fix 1 all npt temp 308 308 20 iso 1 1 1000.0
run 10000

I look at the VdW value at step 0.

I suspect that this may be due to the long range VdW truncations, yet could not find a solution for it.

Marcel Balçık
Istanbul Technical University
marcelbalcik@…24…

MS, I think by default has a much lower cutoff (~10 Angs) which is why you are seeing lower energy. One thing you can do to confirm if truncation is the issue is to create an single molecular in significantly larger cell. Then use the cutoff on both MS and lammps which is largest than your molecular dimensions to include all interactions. Since, it is a single point energy calculation, you can try that. When you do that, both should match.

HTH

Thanks for the answer.

Yet i forgot to mention that, cut off for MS was set to 15 A and also for only one repeat unit of the polymer (in a very big cell) results the same value for VdW Energy.

Same means what you reported or same lammps and MS. ?

MS has something called spline settings beyond cutoff which lammps does not have (I think) which could result in different values. This is why I suggested to increase your cutoff to a lot more than molecule dimensions to that spline corrections do not play a role. Give it a shot.

Other thing, try removing PCFF 001 setting for lammps.

Best Regards,
Vikas

Yes i mean both softwares(MS and LAMMPS) result the same VdW energy value for an alone repeat unit in a very big box.

So you are suggesting to set a cut off value which is higher than the box dimensions?

I could not understand what you mean by removing pcff 001 settings?

Thanks for your answer again

Marcel Balçık

Hi,

I use Materials Studio and LAMMPS simultaneously for a polyimide.

The problem i have is that, while MS Forcite module calculates my
structure's VdW energy as -78.516, in LAMMPS i have -88.7126.

I have checked my pair parameters for so many times and there are no
problems in them.

that is what you say.

in any case, there is a very important piece of information missing
here: you don't specify which version of LAMMPS you are using, and -
even more importantly - the version of msi2lmp
there have been "known" issues with class2 force field support for
quite a while and there have been several updates to msi2lmp recently
that address some of the issues and include more rigorous consistency
checking.
you may just have a data file that is missing parameters.

axel.

I use 30 Sep 13 version of LAMMPS and 12 Apr 13 version of msi2lmp.

I have added all the missing parameters which msi2lmp could not locate in frc file for bond-angle and dihedral parameters. Yet there occured no problem in pair coefficients and i checked my data file and forcefield file after conversion for several times.

Marcel

I use 30 Sep 13 version of LAMMPS and 12 Apr 13 version of msi2lmp.

that is too old a version of msi2lmp. please see:
http://lammps.sandia.gov/bug.html

In the latest version of msi2lmp, there is a problem for dihedral coefficients so i cannot use it. All the dihedral coefficient except the first one are transformed into integers. It was a resolved issue in the past yet it is back with the latest versions.

In the latest version of msi2lmp, there is a problem for dihedral
coefficients so i cannot use it. All the dihedral coefficient except the
first one are transformed into integers. It was a resolved issue in the past
yet it is back with the latest versions.

please provide an example that proves your claim.

none of the test examples here seem to suffer from it.
http://git.icms.temple.edu/git/?p=lammps-icms.git;a=tree;f=tools/msi2lmp/test;hb=HEAD

axel.

In the latest version of msi2lmp, there is a problem for dihedral
coefficients so i cannot use it. All the dihedral coefficient except the
first one are transformed into integers. It was a resolved issue in the past
yet it is back with the latest versions.

btw: i don't see any e-mails by you reporting this issue either to me
or to the mailing list in my e-mail archive...

Actually, i have now seen and remembered that in the latest version of msi2lmp, i have the following problem;

cannot open …\frc_files\pcff

Instead of lloking for the file in the folder i am in, it looks for somewhere else.

Also i can assure you that there are no problems in the pair coefficients. The forcefield and data files i use are also attached.

msi2lmp.jpg

msi2lmp2.jpg

msi2lmp3.jpg

msi2lmp4.jpg

pcffyeni.frc (345 KB)

stablyapi.lammps05 (1.39 MB)

Actually, i have now seen and remembered that in the latest version of
msi2lmp, i have the following problem;

what you are showing me is *not* the latest version of msi2lmp.
please see the attached images for what it should look like.

cannot open ..\frc_files\pcff

Instead of lloking for the file in the folder i am in, it looks for
somewhere else.

the way how msi2lmp finds force field databases has been streamlined
and make more consistent. if you want a specific file to be
recognized, the force field file argument has to contain at least one
slash. otherwise it will look for the central data base directory that
is set up by the windows installer and pointed to with an environment
variable. failing that, it will look for the directory inside the
distribution where the executable was compiled.
please see an example in the second attached screenshot.

this is documented behavior. if you feel the documentation is not
accurate or misleading, i'd be happy to include any edits from anybody
that is willing to improve it.

open source software packages are fundamentally dependent on qualified
feedback from users and particularly contributions to the package, if
only to the documentation. in fact, the importance of _real_ users
contributing to the documentation cannot be underestimated. lots of
things that are "obvious" or "trivial" to a developer do not fall into
those categories for a regular or casual users and thus developers are
often not very qualified to write a good documentation would benefit
massively from users pointing out or rewriting the problematic parts
into proper language.

Also i can assure you that there are no problems in the pair coefficients.
The forcefield and data files i use are also attached.

which are useless without the mdf and car files and the matching lammps input.

axel.

msi2lmp-custom.jpg

msi2lmp-default.jpg