Re: [gmx-users] How to adjust the box size to correct density?

To rescale the box.gro to a desired size using the actual density 543.21 kg/l of the solvent and get a new scaled.gro file, I use this command: $ gmx editconf -f box.gro -density 543.21 -o scaled.gro > logfile On Tue, Jan 5, 2016 at 7:05 PM, Chang Woon Jang wrote: >

Re: [gmx-users] How to adjust the box size to correct density?

Dear Abhishek Khetan, Thank you for your answer. It means that Gromacs does not automatically adjust the box size even though NPT ensemble is employed. Am I right? Different from Gromacs, Lammps automatically adjust box size when NPT ensemble is applied during the simulation. Therefore, the

[gmx-users] How to adjust the box size to correct density?

Dear Gromacs Users, I have a low density polymer system initially. I would like to fit the correct liquid density using NPT simulation. I used Pcoupl=berendsen for 22 ns but the box size in confout.gro is still the same as the input size of conf.gro. Initial in conf.gro (10.0 10.0 9.8) output

Re: [gmx-users] How to adjust the box size to correct density?

Dear Justin, I am curious about resizing the box. My system contains 15000 atoms representing liquid polymer with very low density (maybe gas phase due to very low density). Does this very low density affect the simulation not to converge the box? Or, do the initial conditions

Re: [gmx-users] How to adjust the box size to correct density?

On 1/5/16 1:42 PM, Chang Woon Jang wrote: Dear Abhishek Khetan, Thank you for your answer. It means that Gromacs does not automatically adjust the box size even though NPT ensemble is employed. Am I right? This is incorrect. The box size will change under the influence of pressure.

Re: [gmx-users] How to adjust the box size to correct density?

On 1/5/16 2:25 PM, Chang Woon Jang wrote: Dear Justin, I am curious about resizing the box. My system contains 15000 atoms representing liquid polymer with very low density (maybe gas phase due to very low density). Does this very low density affect the simulation not to converge the box?

[gmx-users] how to adjust the box size to correct density?

Dear Gromacs Users, I have a low density polymer system initially. I would like to fit the correct liquid density using NPT simulation. I used Pcoupl=berendsen for 22 ns but the box size in confout.gro is still the same as the input size of conf.gro. Initial in conf.gro (10.0 10.0 9.8) output

Re: [gmx-users] how to adjust the box size to correct density?

Hi, On Tue, Jan 5, 2016 at 7:15 PM Chang Woon Jang wrote: > Dear Gromacs Users, > > > I have a low density polymer system initially. I would like to fit the > correct liquid density using NPT simulation. > > I used Pcoupl=berendsen for 22 ns but the box size in

Re: [gmx-users] how to adjust the box size to correct density?

Hi, Look at what md.log says about the value for pcoupl it read from your .tpr. :-) Mark On Tue, Jan 5, 2016 at 9:39 PM Chang Woon Jang wrote: > Dear Mark, > > I obtained the tpr file with gro and topology file using grompp -v. > > The following is from md.log file. >

Re: [gmx-users] how to adjust the box size to correct density?

Dear Mark, I see. pcoupl = No is obvious. That means when I create tpr file from grompp.mdp, the pcoupl setting was No instead of berendsen. Thank you very much. Best regards, Changwoon Jang On Tue, Jan 5, 2016 at 3:41 PM, Mark Abraham wrote: > Hi, > > Look at

Re: [gmx-users] How to adjust the box size to correct density?

Dear Justin, Please take a look at the file. I modified mdp file provided from VOTCA tutorial. I think that mdp file is ok. Thank you very much. Best regards, Changwoon Jang On Tue, Jan 5, 2016 at 2:45 PM, Chang Woon Jang wrote: > Dear Justin, > > Please take a

Re: [gmx-users] How to adjust the box size to correct density?

Dear Justin, The following is from .mdf file. ; VARIOUS PREPROCESSING OPTIONS include = define = ; RUN CONTROL PARAMETERS integrator = md ; Start time and timestep in ps tinit= 0 dt = 0.001 nsteps

Re: [gmx-users] how to adjust the box size to correct density?

Dear Mark, I obtained the tpr file with gro and topology file using grompp -v. The following is from md.log file. Best regards, Changwoon Jang Log file opened on Fri Nov 13 13:52:29 2015 Host: c438-702.stampede.tacc.utexas.edu pid: 8923 rank ID: 0 number of ranks: 64 GROMACS: