[gmx-users] Problem with pressure form g_energy

Dear gmx-users, I have experienced the following problem with g_energy program. The problem is the same for at least three versions (3.3.4, 4.0.7 and 4.5.1). When I calculate pressure value (in NPT simulation) using g_energy I obtain the result (average value plus errors, drift etc.) and the

Re: [gmx-users] an example to test mdrun-gpu x mdrun

Hi Alan, On 9/14/10 3:21 PM, Alan wrote: Hi there, I am testing on a MBP 17 SL 10.6.4 64 bits and nvidia GeForce 9600M GT So I got mdrun-gpu compiled and apparently running, but when I try to run 'mdrun' to compare I have a segment fault. Any other comments to the md.mdp and em.mdp are

[gmx-users] force field parameters for lipids on lipidbook.bioch.ox.ac.uk

Hi, readers of this list who are interested in the simulation of membranes, membrane proteins, micelles etc. might be interested in a new web site we recently set up [1]: http://lipidbook.bioch.ox.ac.uk It is a public repository for force field parameters with a special emphasis on

Re: [gmx-users] Problem with pressure form g_energy

Mikhail Stukan wrote: Dear gmx-users, I have experienced the following problem with g_energy program. The problem is the same for at least three versions (3.3.4, 4.0.7 and 4.5.1). When I calculate pressure value (in NPT simulation) using g_energy I obtain the result (average value

Re: [gmx-users] WHAM

Hi Justin, On 17/09/10 11:51, Justin A. Lemkul wrote: Also in section 5.3 is the procedure for how to use REMD data, but I don't think it will ever accomplish what you want. The input into WHAM would be energies, not RMSD vs. R(g), as you initially stated as your goal. You can easily build free

Re: [gmx-users] ACE patch for CHARMM27

Dear Justin, Thank you very much for your quick response, which put me on the right track. Of course, I have some more questions and comments. 1. Putting residues in .rtp means adding ACE to the peptide sequence. This is not the CHARMM convention, where all blocking groups are handled

Re: [gmx-users] ACE patch for CHARMM27

Krzysztof Kuczera wrote: Dear Justin, Thank you very much for your quick response, which put me on the right track. Of course, I have some more questions and comments. 1. Putting residues in .rtp means adding ACE to the peptide sequence. This is not the CHARMM convention, where all

Re: [gmx-users] WHAM

On 18/09/10 18:32, Justin A. Lemkul wrote: Hi Justin, On 17/09/10 11:51, Justin A. Lemkul wrote: Also in section 5.3 is the procedure for how to use REMD data, but I don't think it will ever accomplish what you want. The input into WHAM would be energies, not RMSD vs. R(g), as you initially

[gmx-users] Post doctoral positions available in theoretical physical chemistrymolecular simulation

Hi all, This is just to announce the post doctoral positions available in the University of Rochester, Rochester, NY, United States - http://chem.chem.rochester.edu/~prezhdo_group/PostdocAnnouncement_Prezhdo.pdf -- Dr. Vitaly V. Chaban Department of Chemistry University of Rochester Rochester,

[gmx-users] rerun on gro file

Hi, I'm trying to do rerun on a trajectory which came from catting some gro files of a metadynamics simulation. I simply did trjcat -f 1.gro 2.gro 3.gro -o all.xtc -cat then I used this all.xtc for rerun. the output COLVAR is written but only for one step, I did test on some other trajectory

Re: [gmx-users] rerun on gro file

fahimeh baftizadeh wrote: Hi, I'm trying to do rerun on a trajectory which came from catting some gro files of a metadynamics simulation. I simply did trjcat -f 1.gro 2.gro 3.gro -o all.xtc -cat then I used this all.xtc for rerun. the output COLVAR is written but only for one step, I did

Re: [gmx-users] rerun on gro file

Thank you Justin, I used -settime option and set different starting time, at the end I check xtc file with gmxcheck and the number of fram is ok. But I still have the same problem, I copy what is inside the log file:   Step   Time Lambda   0    0.0   

Re: [gmx-users] rerun on gro file

fahimeh baftizadeh wrote: Thank you Justin, I used -settime option and set different starting time, at the end I check xtc file with gmxcheck and the number of fram is ok. But I still have the same problem, I copy what is inside the log file: Step Time Lambda

Re: [gmx-users] g_wham: Pull geometry direction_periodic not supported

On 9/10/10 Sep 10,2:40 PM, Eudes Fileti wrote: Hi gmx-users I finished a series of pulling runs using the periodic_direction option and when I run the g_wham analysis I received the following message. --- Program g_wham, VERSION 4.5 Source