Dear all,
I want to calculate electrostatic energy of whole system (contains some water molecules as well as two opposite ions) by two methods:
But each of these methods leading to different results in electrostatic energy. May you please explain me why these results differs?
water+ion.in (1.67 KB)
water+ion2.in (1.33 KB)
Dear all,
I want to calculate electrostatic energy of whole system (contains some
water molecules as well as two opposite ions) by two methods:1) by thermo_style command,
2) and by rerun command (post-processing).But each of these methods leading to different results in electrostatic
energy. May you please explain me why these results differs?
because there has to be a difference in the input or data files
somewhere. or you did something else differently.
impossible to say from remote.
axel.
Thank you dear Axel,
But, input and data files for both (the attached files for example) are the same. Please see them. Thanks again.
With Regards
solvate.data (9.29 KB)
solvate-by-rerun.in (781 Bytes)
solvate-by-thermo_style.in (835 Bytes)
Thank you dear Axel,
But, input and data files for both (the attached files for example) are the
same. Please see them. Thanks again.
they are not the same.
if i insert a run 150 into the rerun input and then put them side by
side, there is no significant difference that cannot be explained by
writing out coordinates and velocities with six significant digits.
Thanks again,
In case “rerun”, i intend to remove LJ pair potential (by setting epsilon=0 in pair coeffs in data file) and remain only Coulombic interaction (because I want to calculate Coulombic force on some groups). When I inserted a run 150 before rerun I encountered with this error:
ERROR on proc 0: Out of range atoms - cannot compute PPPM (pppm.cpp:1667)
Whereas In case “epsilon is not equal to zero” there is not error. To avoid the error, Is there any way to prevent to use “run 150”? I mean replace “run 150” by a command such as :
rerun dump.txt first 150 dump x y z vx vy vz ix iy iz box yes replace yes
which contains " first 150".
I tested this command, But it leading to different result in Coulombic energy than before.
This command not been adequately explained in Manual. Thank you.
Yasti
Thanks again,
In case "rerun", i intend to remove LJ pair potential (by setting epsilon=0
in pair coeffs in data file) and remain only Coulombic interaction (because
I want to calculate Coulombic force on some groups). When I inserted a run
150 before rerun I encountered with this error:
ERROR on proc 0: Out of range atoms - cannot compute PPPM (pppm.cpp:1667)
Whereas In case "epsilon is not equal to zero" there is not error. To avoid
of course that happens. it just makes sense.
the error, Is there any way to prevent to use "run 150"? I mean replace "run
150" by a command such as :
rerun dump.txt first 150 dump x y z vx vy vz ix iy iz box yes
replace yes
which contains " first 150".
this makes no sense. you can just drop the "run 150". i only mentioned
to insert the run 150 to make the two log files as comparable as you
claimed.
I tested this command, But it leading to different result in Coulombic
energy than before.
This command not been adequately explained in Manual. Thank you.
this is getting ridiculous. things are properly explained. the problem
is more in your lack of comprehension of the procedure on multiple
levels. it is impossible to write a manual for that.
as far as i am concerned, i consider this issue resolved.
axel.
Dear Axel,
Thanks for your attentions. The issue resolved to me by adding another dump file produced in the first run in the case “thermo_style” then it is inserted to input file instead of “run 150” in the case “rerun”.
But also, That is not getting ridiculous…
Yasti