Re: [gmx-users] About Pulling code in Gromacs 5.0.2

2015-06-10 Thread Alex
The artifacts warning is general (mentioned in the manual) and has nothing to do with your system (aside from your mdp), everyone using absolute reference frame gets this warning. That said, the error you're getting is actually descriptive. So: 1. Check if the system is stable and happy without

Re: [gmx-users] Different Cv and Cp

2015-06-10 Thread Faezeh Pousaneh
Dear Michael, Could you please comment on my last question, thanks a lot. I have noticed that when I run both NVT and NPT simulations from a same .gro file (obtained from energy minimization) I obtain same Cv and Cp for two ensembles. However, so far I was running NVT after NPT (meaning I used

Re: [gmx-users] g_wham error in umbrella simulation

2015-06-10 Thread Ming Tang
Hi,高 发银行卡号给我,我还你钱,你结婚肯定要用钱吧 Sent from my Huawei Mobile Ming Tang m21.t...@qut.edu.au wrote: Dear all, I am doing an umbrella simulation, and come across the following error. Command line: g_wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kCal -b 2000 Found 27 tpr and 27 pull

Re: [gmx-users] GPU acceleration

2015-06-10 Thread Szilárd Páll
PS: if you are very concerned about cooling why not look at some gaming benchmarks of GTX 960 boards by different manufacturers and pick the one with the best cooling, e.g. here's one such review: http://www.tomshardware.com/reviews/evga-super-super-clocked-gtx-960,4063-4.html -- Szilárd On Wed,

Re: [gmx-users] Different Cv and Cp

2015-06-10 Thread Michael Shirts
I can't diagnose what is wrong in every case; I can just say that statistical mechanics says that both methods for calculating Cv and both methods for calculating Cp should agree within noise. On Wed, Jun 10, 2015 at 8:54 AM, Faezeh Pousaneh fpoosa...@gmail.com wrote: Dear Michael, Could you

Re: [gmx-users] GPU acceleration

2015-06-10 Thread Szilárd Páll
On Wed, Jun 10, 2015 at 4:21 AM, Alex nedoma...@gmail.com wrote: At this point, we will be getting the card for sure, likely the GTX 960 you suggested. Hence, a question. Which of the manufacturers would you recommend in terms of cooling (if you think it might become an issue with week or so

Re: [gmx-users] Different Cv and Cp

2015-06-10 Thread André Farias de Moura
Dear Faezeh, Michael is absolutely right, both methods should yield exactly the same Cp and Cv values, but that is only true in the limit of infinite sampling. If sampling is not infinite but is long enough, Cp and Cv values should agree within the statistical uncertainty of each method. So it

Re: [gmx-users] Questions about the topology file format

2015-06-10 Thread Sotirios Dionysios I. Papadatos
If I am not mistaken, and there is a chance that I am the length and force constant are used with grompp in ffbonded.itp in the force field directory. After the question mark everything else is indeed not read so it is mostly used by the users for clarification. But I believe that in the part

Re: [gmx-users] creating index for first hydration layer water molecules

2015-06-10 Thread Sahithya S Iyer
Thanks for the reply Justin. I have tried the following: g_select -f prodrun.xtc -s prodrun.tpr -n index.ndx -os size.xvg - oc cfrac.xvg -oi index.dat -select 'Nearby water resname SOL and within 0.35 of group Protein' But there is a syntax error. Could you please tell me where i could be going

Re: [gmx-users] which file to use to analyze trajectory using code

2015-06-10 Thread Sahithya S Iyer
Thanks Oliver ! On Tue, Jun 9, 2015 at 7:24 PM, Oliver Stueker ostue...@gmail.com wrote: ​Hello Sahithya, the xdrfile library is only one of many ways to write your own code trajectory analysis. Other options are: - Use share/gromacs/template/template.cpp ( template.c for Gromacs

Re: [gmx-users] GPU acceleration

2015-06-10 Thread Alex
Well, I've had a Gigabyte-made OC'd GTX 660 at home (for gaming) for a few years, no problems at all. I guess my question was more along the lines of whether GPU MD runs are equivalent to week-long gaming in terms of heat production. What I also didn't know is whether 960 was a fiery beast. Your

[gmx-users] Radius of gyration

2015-06-10 Thread ??????
Dear gromacs experts, I tried to analysis the Radius of gyration of a polymer. But I found the result of first frame was always very different. Then I installed different vesions of gmx with or without mpi. And I got different results. So I used the first tutorial on

[gmx-users] Ion binding to DNA

2015-06-10 Thread soumadwip ghosh
Hello, I am asked by one of the reviewers of my paper about the distribution of ions ( Mg2+) bound to a single stranded DNA as a function of simulation time at different salt concentrations. In order to do that I have calculated the RDF of ions from the closest atom of DNA using g_rdf