[gmx-users] Wall option with 12-6 LJ

Dear all, I am trying to apply wall options using 12-6 LJ potential. Right now I am using isotropic Berendsen pressure coupling, my first question is, is that the correct method? When I tried to use semi isotropic pressure coupling, the box dramatically expanded. And below is the simulation o

[gmx-users] Re: Re: unwrap trajectory file using -pbc nojump

e specific > than "Re: Contents of gmx-users digest..." > > > Today's Topics: > > 1. unwrap trajectory file using -pbc nojump (Yutian Yang) > 2. Re: unwrap trajectory file using -pbc nojump (Tsjerk Wassenaar) > 3. Re: Re: Lennard-Jones potential for protons (

[gmx-users] unwrap trajectory file using -pbc nojump

Dear all, I want to remove PBC effects for my system and calculate the diffusion coefficient. I am using Gromacs 4.5.4. My system is a 15 nm cubic box with 376 polymer chains each with 28 beads. The simulation time is about 2000 ns. However, when I use the command trjconv_mpi -f all.xtc -s

[gmx-users] PBC problem

Hi all, I have a question about PBC. If I have a polymer chain that is longer than the box length, will the properties of the chain change because the tail of the chain may interact with the head of the chain due to PBC? Thank you! Yutian -- gmx-users mailing listgmx-users@gromacs.org htt

[gmx-users] Re: MSD and frequency of writing trajectories

Erik, Do you mean that if the particle diffuses too fast, it will appear like it doesn't move because of the PBC? I have another issue. If I have a polymer chain with the length almost the same as the box length. It is possible that the COM diffusion of the chain may appear it does not move

[gmx-users] Velocity autocorrelation problem

Dear all, I am trying to use g_velacc to calculate diffusion coefficient for a single polymer chain. As I follow the Gromacs tutorial and use the command (version 4.5.1) g_velacc -acflen 1001 -nonormalize -mol -n atoms.ndx -s topol.tpr the ACF is always zero. However, if I remove -mol option,

[gmx-users] g_msd problem

it also a bug in the program or have I done something wrong on the command? Thank you! Best Regards Yutian Yang -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/S

[gmx-users] RE: gmx-users Digest, Vol 109, Issue 112

. Is it also a bug in the program or have I done something wrong on the command? Thank you! Best Regards Yutian Yang From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of gmx-users-requ...@gromacs.org [gmx-users-requ.

[gmx-users] Can Gromacs do oscillatory shear?

Hi all, I am trying to preform oscillatory shear flow on Gromacs. Is there any existing commands/codes to do it or do I have to modify the code myself? If I have to modify code, where can I find the source code for deform? Thank you so much! Shirley Young -- gmx-users mailing listgmx-use

[gmx-users] Fwd: Large pressure fluctuation

> Hi all, > > I have some problems with the pressure of my system. When I try to run > equilibrium systems (NVT or NPT), I have got large pressure fluctuations (2 > or 3 orders higher than average value). When I apply shear to the system, the > pressure of the system increases with the increa