Re: [gmx-users] REMD - step 12005: Water molecule starting at atom 7030 can not be settled

OK, but with Berendsen you're also not observing physics. Your call. Mark On Wed, May 14, 2014 at 3:50 AM, Steven Neumann s.neuman...@gmail.comwrote: Thanks a lot! Berendsen barostat works well with V-rescale using REMD, no crashes observed. On Tue, May 13, 2014 at 2:08 PM, Mark Abraham

[gmx-users] Why does the list keep unsubscribing me?

This is the second time in 2 months, that I am unsubscribed from the list and i have to subscribe again. I just get an email that you have been unsubscribed from the list? How can I get unsubscribed without my intervention is beyond understanding? --

[gmx-users] TIP5P water and Test Particle Insertion

Dear Gromacs users, I am using Test Particle Insertion with Gromacs 4.6.5. The method works well when I use TIP3P and SPC/E water to obtain the excess chemical potential of water and I get a reasonable agreement with experimental data. However, when using TIP5P water the method diverges:

Re: [gmx-users] Can't make links on GROMACS

So Google Groups doesn't allow you to import users, right? But I have seen Gromacs's Google Groups, however it has been abandoned since 2012, I don't know why. Also, I found another mail list which is better than the three ones I have mentioned above. It www.gmane.org. It also has statistic of

[gmx-users] pbc problem

dear gromacs users i did simulate zinc and copper ion on human growth hormone protein when i saw my md.gro and md.xtc files by VMD software i found out my system isn,t in the box(cubic) i tried to solve this problem by : trjconv -f md.xtc -s md.tpr -o new.xtc -n index.ndx -pbc mol but there is

Re: [gmx-users] Why does the list keep unsubscribing me?

Hi, Someone else mentioned the same recently. Automatic removal can happen if someone, e.g. a spammer, sends a mail to gmx-users-unsubscr...@gromacs.org while faking your email address in the From: field. Mailman is now maintained centrally by the university, so I can't dig in the logs for

Re: [gmx-users] why two GTX780ti is slower?

Hi Mark: thanks a lot for the messages. In most cases, job failed with following messages if I used intel MPI to evoke two GPU: [mpiexec@cudaA.compuBio] HYDU_getfullhostname (./utils/others/others.c:136): getaddrinfo error (hostname: cudaA.compuBio, error: Name or service not known)

Re: [gmx-users] why two GTX780ti is slower?

This just tells that two GPU-s were detected but only the first one was automatically selected to be used - presumably because you manually specified the number of ranks (-np or -ntmpi) to be one. However, your mail contains neither the command line you started mdrun with, nor (a link to) the log

[gmx-users] question

Dear Gromacs users After I calculated the secondary structure of residues from 1 to 59 using do_dssp during 20 ns MD simulation, I used xpm2ps to show the picture with ps.m2p. y-axis is true but x- axis is very long. My ps.m2p file is as follows: ; Command line options of xpm2ps override the

Re: [gmx-users] why two GTX780ti is slower?

Hi Szilárd: thx for the comments. The log file in my previous thread comes from command line: tmp/input mpirun -np 2 mdrun_mpi -s 4.tpr [mpiexec@cudaA.compuBio] HYDU_getfullhostname (./utils/others/others.c:136): getaddrinfo error (hostname: cudaA.compuBio, error: Name or service not known)

Re: [gmx-users] Ion concentration of genion vs charmm-gui

By hand it is about 201 molecules. It is strange that the membrane builder in charmm-gui gives a different answer for the same box dimensions. I guess those of us that use the charmm-gui membrane builder should keep this in mind. On Wed, May 14, 2014 at 11:14 AM, Erik Marklund

Re: [gmx-users] Ion concentration of genion vs charmm-gui

On 5/14/14, 12:06 PM, Ali Khan wrote: By hand it is about 201 molecules. It is strange that the membrane builder in charmm-gui gives a different answer for the same box dimensions. I guess those of us that use the charmm-gui membrane builder should keep this in mind. Better yet, please

[gmx-users] amber to gromacs conversion of LJ potential

Dear All, While converting LJ parameters from Amber to Gromacs, acpype tool (that is used for converting Amber input files into those for gromacs) uses following form: sigma = 2 * r * 2^(-1/6) I understand the factor 2^(-1/6), but there is another 2 that appears in the beginning. Where is that

[gmx-users] flat-bottomed potentials

Hi Dear Gromacs Users, I am running a umbrella samplimg simulation with gromacs 4.6.5, this simulations is a molecule permeating an ion channel, i decided to use X Y position restraints 400KJ , but i am not pretty sure if this kind of bias if a real mistake, i was wondering if anyone know how to

Re: [gmx-users] Why does the list keep unsubscribing me?

Thanks for the explanation Rossen.I hope mailman gets some more artificial intelligence in coming future :).cheers,Abhi Date: Wed, 14 May 2014 14:33:00 +0200 From: ros...@kth.se To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Why does the list keep unsubscribing me? Hi, Someone else

Re: [gmx-users] Positive energy .

Hello Justin, I looked at the energy components. What I find is that Short Range LJ is highly positive (208522 kJ/mol) . Also the short range coulomb interaction (-2028.46 kJ/mol) , although negative looks weak (I think so , because an earlier minimization of a system with methane( oplsaa) in