Data file generation problem

Hi All,
I have a problem in generating data file which I’d appreciate it if you help me to solve it. For preparing a simulation I need a to move a molecule to a specific location and equilibrating the system and then generating a new data file for further simulations. I have tried different scenarios to make the data file but all failed except one. By the way I’m using lammps-icms which I pulled March 20.
Below are the styles that are used in my input file:

atom_style full
bond_style harmonic
angle_style charmm
dihedral_style charmm
improper_style harmonic
pair_style lj/charmm/coul/long

Here is the list of my trials:

  1. write_data :
    I ran the simulation for designated time steps and after that I used :
    write_data filename.data
    run 0
    This gives me a data file but the problem is that it writes some negative types in the Dihedrals section which makes the data file not to be usable. I was wondering where those negative types are coming from?

  2. dump dcd :
    I dumped a dcd file at the desired time step and then I used dcd and psf file to open it in vmd generate a data file in vmd by using topo writelammpsdata command. This gives me a data file with incorrect number of bonds, angles, dihedrals types and the first few lines of it is as below:

LAMMPS data file. CGCMM style. atom_style full generated by VMD/TopoTools v1.2 on Wed May 21 13:33:07 CDT 2014
24497 atoms
18136 bonds
16406 angles
13660 dihedrals
350 impropers
11 atom types
1 bond types
1 angle types
1 dihedral types
1 improper types
-25.467230 24.532770 xlo xhi
-24.936508 25.063492 ylo yhi
-48.315960 48.084209 zlo zhi

Pair Coeffs

1 C2O2

2 C301

3 C321

4 C331

5 CX

6 HGA2

7 HGA3

8 HT

9 O2D1

10 O302

11 OT

Bond Coeffs

1

Angle Coeffs

1 unknown

Dihedral Coeffs

1 unknown

Improper Coeffs

1 unknown

What’s the problem? Isn’t a dcd loaded with psf enough for generating data file with topotools.

  1. I read dcd and psf file in vmd and I saved a pdb from the desired frame. I used charmm2lammps tool to generate a data file using the psf, charmm parameter file, charmm topoloy file and the generated pdb file. This one gives me a clean working data file.

I appreciate your help.

Cheers,
Kasra.

Hi All,
I have a problem in generating data file which I'd appreciate it if you
help me to solve it. For preparing a simulation I need a to move a molecule
to a specific location and equilibrating the system and then generating a
new data file for further simulations. I have tried different scenarios to
make the data file but all failed except one. By the way I'm using
lammps-icms which I pulled March 20.

problem report ​rule #1: update to the latest version and see, if the
problem persists.​ if it does, you massively increase the chances that
somebody will look into it.

in any case: ​why do you need a data file​ for this? the simplest way to
move an object in LAMMPS to a different location are either fix move or fix
smd and a (short) simulation (assuming a dense system).

Below are the styles that are used in my input file:

atom_style full
bond_style harmonic
angle_style charmm
dihedral_style charmm
improper_style harmonic
pair_style lj/charmm/coul/long

  Here is the list of my trials:

1. write_data :
I ran the simulation for designated time steps and after that I used :

                                        write_data filename.data

                                        run 0
This gives me a data file but the problem is that it writes some negative
types in the Dihedrals section which makes the data file not to be usable.
I was wondering where those negative types are coming from?

​again, first test against the latest version. if the problem persist,
produce the smallest possible input that demonstrates the issue.​

2. dump dcd :
I dumped a dcd file at the desired time step and then I used dcd and psf
file to open it in vmd generate a data file in vmd by using topo
writelammpsdata command. This gives me a data file with incorrect number of
bonds, angles, dihedrals types and the first few lines of it is as below:

  LAMMPS data file. CGCMM style. atom_style full generated by
VMD/TopoTools v1.2 on Wed May 21 13:33:07 CDT 2014

​this is an outdated version of topotools plugin. you have to update VMD to
a recent alpha test version which has the latest topotools bundled and also
bugs in the supporting VMD code components fixed. those are problems that
are related to reading topology data, so you may be affected by it.​

24497 atoms
18136 bonds
16406 angles
13660 dihedrals
350 impropers
11 atom types
1 bond types
1 angle types
1 dihedral types
1 improper types
-25.467230 24.532770 xlo xhi
-24.936508 25.063492 ylo yhi
-48.315960 48.084209 zlo zhi

# Pair Coeffs
#
# 1 C2O2
# 2 C301
# 3 C321
# 4 C331
# 5 CX
# 6 HGA2
# 7 HGA3
# 8 HT
# 9 O2D1
# 10 O302
# 11 OT

# Bond Coeffs
#
# 1

# Angle Coeffs
#
# 1 unknown

# Dihedral Coeffs
#
# 1 unknown

# Improper Coeffs
#
# 1 unknown

  What's the problem? Isn't a dcd loaded with psf enough for generating
data file with topotools.

​i don't know and i cannot say without having a small test case.​ for
certain, VMD cannot write the multiple "*Coeffs" sections, since that
information is neither stored in the .dcd file (that has only coordinates)
not the .psf file (that has only the definition of the bond topology, not
the parameters. they are read by charmm (or namd) later from a parameter
file.

axe;/