[gmx-users] Restart a run with different files

2012-12-23 Thread Davit Hakobyan
Dear Gromacs users, I use Gromacs 4.5.1. The problem relates to the restarting procedure of a run. Usually I restart the run with the -append option and now I need to move the .trr and .xtc files to another directory since they got too big for the directory quota where they were located by

Re: [gmx-users] Restart a run with different files

2012-12-23 Thread Justin Lemkul
On 12/23/12 3:21 AM, Davit Hakobyan wrote: Dear Gromacs users, I use Gromacs 4.5.1. The problem relates to the restarting procedure of a run. Usually I restart the run with the -append option and now I need to move the .trr and .xtc files to another directory since they got too big for

[gmx-users] exact average distances with g_mdmat

2012-12-23 Thread IsaureCB
Dear gmx-users, I would like to select, for each residue of a model, the residues that are within 3.6 A in average over a simulation. g_mdmat must create this information at some point while generating the contact diagrams, but I would like to extract the real values before they are

[gmx-users] free energy

2012-12-23 Thread mohammad agha
Dea GROMACS Users, I want to calculate the free energy for my system, for example (Gibbs and Helmholtz), but I didn't define the free_energy in the md.mdp and my simulation has been finished!!! May I ask you that say me is there a solution fro this problem? Best Regards Sara -- gmx-users

Re: [gmx-users] Metadynamics with Esential Dynamics Sampling

2012-12-23 Thread James Starlight
by the way it's also interesting to me if there are any other possible ways to obtain representation of the free energy surfaces in the essential coordinates subspace ? Might the methods like Ubrella sampling ( with applied PMF in the pulling direction along selected eigenvector ) or flooding

Re: [gmx-users] voltage for membrane?

2012-12-23 Thread Peter Lai
Albert mailmd2...@gmail.com wrote: Dear all: As we know that many membrane has a membrane potential with typical range from -40mV to 80mV. I am just wondering is it possible to add voltage for membrane protein simulation in Gromacs? If yes, and how? I go through the .mdp documentation and

Re: [gmx-users] voltage for membrane?

2012-12-23 Thread Peter Lai
Yun Shi yunsh...@gmail.com wrote: Interesting. Would that be like adding sodium chloride on one side of the membrane while adding only potassium on the other side? On Sun, Dec 23, 2012 at 8:37 AM, Peter Lai p...@uab.edu wrote: Albert mailmd2...@gmail.com wrote: Dear all: As we know that

Re: [gmx-users] voltage for membrane?

2012-12-23 Thread Martin Hoefling
Am 23.12.2012 21:05, schrieb Peter Lai: You can have a look at http://www.ncbi.nlm.nih.gov/pubmed/21843471 , maybe that does what you want. Best Martin Yun Shi yunsh...@gmail.com wrote: Interesting. Would that be like adding sodium chloride on one side of the membrane while adding only