Re: [gmx-users] problem with MPI,thread and number of CPU

Hi, On Mon, May 16, 2016 at 9:13 PM wrote: > > > > p { margin-bottom: 0.1in; line-height: 120%; }a:link { } > > > Dear Gromacs users > > > During simulating DPPC membrane I confront with several Problems. I > intend to express them here and I

[gmx-users] problem with MPI,thread and number of CPU

p { margin-bottom: 0.1in; line-height: 120%; }a:link { } Dear Gromacs users During simulating DPPC membrane I confront with several Problems. I intend to express them here and I really appreciate it if you help me. Briefly I started to simulate a DPPC containing 2000 W and

[gmx-users] improper .gro file format generated by trjconv

Dear gromacs users; I am trying to perform micelle clustering analysis as described in gromcas website: 1. use trjconv -pbc cluster to obtain a single frame that has all of the lipids in the unit cell. This must be the

[gmx-users] tutor/speptide

Dear Gromacs user, In below link where the S-peptide has been taught for the beginner, they point out that the tutorial materials have been stored in the directory "tutor/speptide", would you please let me know where I can find this directory or have access to this directory?

Re: [gmx-users] tutor/speptide

On 5/16/16 9:51 AM, Alexander Alexander wrote: Dear Gromacs user, In below link where the S-peptide has been taught for the beginner, they point out that the tutorial materials have been stored in the directory "tutor/speptide", would you please let me know where I can find this directory or

Re: [gmx-users] Calculating Distance

On 5/16/16 3:20 AM, Sanket Ghawali wrote: Dear, gmx-users, Hello everyone, I'm simulating a peptide in an SDS micelle. The simulation was performed for 100ns When I visualize the trajectory in VMD, the peptide moves to the SDS interface where initially it was placed in the center, the

Re: [gmx-users] simulation_time

On 5/16/16 12:23 AM, Ms. Nikita Bora wrote: Original Message Subject: Re: simulation_time From:"Ms. Nikita Bora" Date:Mon, May 16, 2016 9:42 am To: nik...@tezu.ernet.in

[gmx-users] heat of vaporization

Hi all I am trying to calculate heat of vaporization of tri-ethyl phosphate (tep). I took 500 tep molecules for MD simulation. After energy minimization and NVT I performed NPT simulation for 10ns with usual PBC, dispersion correction etc. >From the final results using g_energy -nmol 500 I got

Re: [gmx-users] Restart simulation from checkpoint file with fewer nodes

Hi all, After spending time for troubleshooting, I found that gromacs checkpoint/restart feature is working well. The failure occurred because I use root user to submit restart job (using slurm resource manager). After switching to non root user, the restart process is running. The reason why I

Re: [gmx-users] Removing periodic boundary condition

Hi Sanket, Can you check the structure in the tpr file (editconf -f .tpr -o .gro/.pdb)? If that is good, then -pbc nojump should work. For the second pass, you shouldn't need -pbc mol then. Cheers, Tsjerk On May 16, 2016 9:06 AM, "Sanket Ghawali" wrote: > Dear,

Re: [gmx-users] Calculating Distance

choose a atom, then calculate the transition vector of it with use of the initial and final coordinate. On Mon, May 16, 2016 at 11:50 AM, Sanket Ghawali wrote: > Dear, gmx-users, > > Hello everyone, > I'm simulating a peptide in an SDS micelle. The simulation was >

[gmx-users] Calculating Distance

Dear, gmx-users, Hello everyone, I'm simulating a peptide in an SDS micelle. The simulation was performed for 100ns When I visualize the trajectory in VMD, the peptide moves to the SDS interface where initially it was placed in the center, the results are as expected. I would like to calculate

[gmx-users] Removing periodic boundary condition

Dear, gmx-users, Hello everyone, I'm simulating a peptide in an SDS micelle. The simulation was performed for 100ns When I view the trajectory in VMD, a portion of the SDS micelle moves to the right and goes into the next box. Of course, because of periodic boundary conditions. I tried using