Re: [gmx-users] Qestion about how to define groups by chain id in a protein ?

Liu Shiyong wrote: Hi, We have a protein with two chains A and B. We want to calculate the interaction energy only. Would you advise how to define the energy groups for the chains and how to output the interaction energy between chains A and B ? Have a search of the mailing list archives,

[gmx-users] Qestion about how to define groups by chain id in a protein ?

Hi, We have a protein with two chains A and B. We want to calculate the interaction energy only. Would you advise how to define the energy groups for the chains and how to output the interaction energy between chains A and B ? -- Shiyong Liu Postdoc center for bioinformatics in the university o

Re: [gmx-users] is there any Problem in V. 3.3.3?

Hi Bala, My guess is you're running with position restraints on. Check the manual. And while you're at it, google for "how to ask questions the smart way". Tsjerk On Fri, Jan 16, 2009 at 3:00 PM, bala ms wrote: > Hi > I am new to Gromacs, I am using V3.3.3. I have run the MD simulation > (

[gmx-users] CNS to Gromos87

Hello, Does anyone know of a script that can convert CNS topology files to Gromacs format? Thanks, Candice Viddal __ Instant Messaging, free SMS, sharing photos and more... Try the new Yahoo! Canada Messenger at http://c

Re: [gmx-users] Rugged dgdl curve in turning off/on the charge for Leu

friendli wrote: > Dear all, > > When I performing mutation free energy calculation from Leu to Ala, I > first turn off the charge on the side chain of Leu. As I read from the > GMX archive, the dG/dl curve should be rather smooth for turning off the > partial charge. > In this step(charge off/on)

[gmx-users] example lookup tables

Hi, The example lookup tables in the directory share/top, table6-8.xvg table6-9.xvg table6-10.xvg table6-11.xvg table6-12.xvg, are all identical. So, which of the vdw potentials is tabulated here? Thanks, Sam Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm __

[gmx-users] Pull code - 2

Hello, I was running different simulations with the following pull code 1/ ;---PULL CODE - pull= umbrella pull_geometry = direction pull_group1 = r_535 pull_vec1 = 0.51 0.026 0.273 pull_k1 = 110 pull_rate1 = 0.002 ; nm/ps = 20 A/ns

[gmx-users] is there any Problem in V. 3.3.3?

Hi I am new to Gromacs, I am using V3.3.3. I have run the MD simulation (using explicit solvent) for 1ns for my protein of interest and also the examples which has given in the Manual. I am getting same kind of graph for the both proteins by plotting CA vs time. The graph shows RMSD value l

[gmx-users] Re: GROMACS 4.0.2 error Value of 'multiplicity' in Proper Dih. is 0

No, David, I get no warnings at all. Is there a way to make warnings more explicit ? Thank you -Himanshu On Tue, 13 Jan 2009, gmx-users-requ...@gromacs.org wrote: Send gmx-users mailing list submissions to gmx-users@gromacs.org To subscribe or unsubscribe via the World Wide Web, vi

RE: [gmx-users] Inconsistent shifts Problem when using g_rdf

> Date: Fri, 16 Jan 2009 09:06:43 +0100 > From: sp...@xray.bmc.uu.se > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] Inconsistent shifts Problem when using g_rdf > > Lin, Pohan wrote: > > I am running NPT simulations by using Parrinello-Rahman pressure > > coupling on Gromacs 3.3.3. My

Re: [gmx-users] Inconsistent shifts Problem when using g_rdf

Lin, Pohan wrote: I am running NPT simulations by using Parrinello-Rahman pressure coupling on Gromacs 3.3.3. My system contains epoxy and cross-linker molecules. By modifying the topology file (add bond, angle, torsion terms in topology), all the molecules are connected together to be an hu