Re: [gmx-users] regarding tha langevin thermostat (integrator sd)

Hi, On Thu, May 11, 2017 at 11:45 PM Felix Y Yang wrote: > Hello, > > I am trying to use a Langevin Thermostat to only heat up a specific group > of atoms in my molecule specified by an index file, while not doing > anything to the rest of the system (grouped as another group

[gmx-users] regarding tha langevin thermostat (integrator sd)

Hello, I am trying to use a Langevin Thermostat to only heat up a specific group of atoms in my molecule specified by an index file, while not doing anything to the rest of the system (grouped as another group in the index file). Is there any way I can achieve this effect? Can I set up

Re: [gmx-users] RMSF problem

Dear Justin Lemkul, Thank’s for prompt reply. My protein has 198 aminoacides (PDB: 2GOJ; http://www.rcsb.org/pdb/explore.do?structureId=2GOJ). After RMSF command (gmx rmsf -f .xtc -s .tpr -o .xvg -res), the output has only 103 aminoacides as visualized by Grace software. I am running gromacs

Re: [gmx-users] RMSF problem

On 5/11/17 1:21 PM, Franco Henrique wrote: Dear, I am have problem with RMSF data, because after I apply this command-line: gmx rmsf -f xxx.xtc -s yyy.tpr -o zzz.xvg -res, the .xvg file has not all residues of protein. If possible, I would like to know a tip to solve this problem. How

Re: [gmx-users] ligand moving out during umbrella sampling

On 5/11/17 1:25 PM, abhisek Mondal wrote: Alright. I'm trying as per your advice. Actually my system is pretty big and due to constraint of computation power it is taking me more time to test vector setup. I really appreciate your time. Thanks a lot for your suggestions. One thing I'm worried

Re: [gmx-users] ligand moving out during umbrella sampling

Alright. I'm trying as per your advice. Actually my system is pretty big and due to constraint of computation power it is taking me more time to test vector setup. I really appreciate your time. Thanks a lot for your suggestions. One thing I'm worried about here. In previous mail, I mentioned the

[gmx-users] RMSF problem

Dear, I am have problem with RMSF data, because after I apply this command-line: gmx rmsf -f xxx.xtc -s yyy.tpr -o zzz.xvg -res, the .xvg file has not all residues of protein. If possible, I would like to know a tip to solve this problem. Best regards, Franco Henrique. -- Doutor em

Re: [gmx-users] Regarding simulation radioactive material

Again, please keep the discussion on the mailing list. On 5/10/17 9:47 PM, RAHUL SURESH wrote: Dear Justin Thank you. I have to think over it a lot. To reparametarise a whole protein, I do not think it's possible or an easy job. The next pull down is the Change is mass should correspond to

Re: [gmx-users] Using the md integrator for calculating free energy of solvation

On 5/11/17 9:49 AM, Dan Gil wrote: Thank you Dr. Lemkul, The simulations ran, but I have some a question about the results. Is it natural to have a nonzero mass_lambda dH/dL? My intuition was that the potential energy does not depend on mass, and my thinking was that the mass contribution

Re: [gmx-users] ligand moving out during umbrella sampling

On 5/11/17 9:21 AM, abhisek Mondal wrote: On Thu, May 11, 2017 at 11:02 AM, abhisek Mondal wrote: Hi, Thank you for the explanation. It really cleared some concepts. But I'm still having my ligand moving in this step. I have modified the code as: ; Pull code pull

Re: [gmx-users] Inconsistence of SPC/E and TIP4P water in Gromacs

On 5/11/17 1:53 AM, Mark Abraham wrote: Hi, On Thu, May 11, 2017 at 3:31 AM ZUO Taisen wrote: Hi guys: I have compared the SPC/E and TIP4P water of the opls force field in Gromacs.But there is something inconsistent of the potential energy in the system The

Re: [gmx-users] assignment of atomname1 and atomname2 in param_example file in GridMAT-MD

On 5/11/17 5:24 AM, manindersingh rajawat wrote: Dear GROMACS users, I have set up a system for membrane simulation. Membrane contains 103 POPC and 25 POPS molecules. I am using GridMAT-MD for calculating area per lipid and thickness of the membrane by following GridMAT-MD tutorial. But

Re: [gmx-users] Calculation of dielectric constant

Thanks a lot Philip for your suggestion. On 11 May 2017 at 13:41, Philip Loche wrote: > Hey Saumyak, > > g_dipoles applies the formula derived by Neumann ( > http://dx.doi.org/10.1080/00268978300102721), which is proportional to > 1/V (box volume) and can not applied

Re: [gmx-users] How to use "gmx view" on Ubuntu?

Dear Justin, Mark and Frank, Thank you so much for explaining it. Now I think I understand it. I was confusing because I thought, I should install/compile the xorg-dev by using "cmake". But actually, what you meant is, use "cmake" to compile Gromacs after installing xorg-dev. I tried as

Re: [gmx-users] Using the md integrator for calculating free energy of solvation

Thank you Dr. Lemkul, The simulations ran, but I have some a question about the results. Is it natural to have a nonzero mass_lambda dH/dL? My intuition was that the potential energy does not depend on mass, and my thinking was that the mass contribution should be very small, if not zero. Best

Re: [gmx-users] ligand moving out during umbrella sampling

On Thu, May 11, 2017 at 11:02 AM, abhisek Mondal wrote: > Hi, > > Thank you for the explanation. It really cleared some concepts. But I'm > still having my ligand moving in this step. I have modified the code as: > ; Pull code > pull= umbrella >

Re: [gmx-users] Running Gromacs on GPUs

Hi, Each of the four simulations on your node has its own particle-particle rank, and we knew that having multiple of them didn't work in 5.1.x, so disabled it. But it was fixed for the 2016 release. Mark On Thu, 11 May 2017 13:00 Giannis Gl wrote: > Dear Gromacs users, >

[gmx-users] Running Gromacs on GPUs

Dear Gromacs users, I am trying to run a multiple walkers metadynamics simulation on Gromacs 5.1.4 using a machine that has 12 CPUs and 4 GPUs. I have compiled Gromacs using the following schems: cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_MPI=on -DGMX_GPU=on

[gmx-users] assignment of atomname1 and atomname2 in param_example file in GridMAT-MD

Dear GROMACS users, I have set up a system for membrane simulation. Membrane contains 103 POPC and 25 POPS molecules. I am using GridMAT-MD for calculating area per lipid and thickness of the membrane by following GridMAT-MD tutorial. But confused how and what to assign in atomname1 and atomname2

Re: [gmx-users] Calculation of dielectric constant

Hey Saumyak, g_dipoles applies the formula derived by Neumann (http://dx.doi.org/10.1080/00268978300102721), which is proportional to 1/V (box volume) and can not applied in your case. According to your description you should consider to calculate a dielectric profile around your protein. If

[gmx-users] Open GROMACS researcher position in Stockholm

Hi, Normally we don’t allow job announcements on these lists, with the one exception for jobs that are directly related to GROMACS developement - and I’m happy to announce that we have a new opening at the main GROMACS site in Stockholm with application deadline June 16! In particular, this is

Re: [gmx-users] soft "exit"

Thank you Mark. That's very helpful Vangelis On Thu, May 11, 2017 at 10:00 AM, Mark Abraham wrote: > Hi, > > On Thu, May 11, 2017 at 8:54 AM Daskalakis Vangelis > wrote: > > > Dear all, > > I am running Gromacs 5.1.4 on a cluster with SLURM

Re: [gmx-users] soft "exit"

Hi, On Thu, May 11, 2017 at 8:54 AM Daskalakis Vangelis wrote: > Dear all, > I am running Gromacs 5.1.4 on a cluster with SLURM workload manager. How > can I terminate the running gromacs jobs (i.e. send the TERM/ INT signals) > but also allow time for each job to "soft

[gmx-users] soft "exit"

Dear all, I am running Gromacs 5.1.4 on a cluster with SLURM workload manager. How can I terminate the running gromacs jobs (i.e. send the TERM/ INT signals) but also allow time for each job to "soft exit" on the next step ? By "soft exit" I mean that the job should be like it is finished (all the