Re: [gmx-users] Scaled 1-5 interactions

Florian Dommert wrote: * Mark Abraham mark.abra...@anu.edu.au [2009-06-05 10:31:22 +1000]: Borys Szefczyk wrote: Dear GROMACS Users, I would like to use the OPLS force field, but with additional scaling factor for the Coulomb 1-5 interactions for certain atoms. More precisely, I want to use

[gmx-users] Reg. g_density

Hey everyone, I would like to know from where does the g_density read the masses and radii of atoms to calculate the density... We do provide a tpr file but from where does it refer to and add these masses... I have a system for which i have a topology... i use this for the generation of tpr but

Re: [gmx-users] Reg. g_density

Hi Jagan, If you provide a .tpr file, the masses will be read from there. Otherwise, when providing a .gro/.pdb file or so, masses will be read from the file atommass.dat in the GMX library directory. Cheers, Tsjerk On Sat, Jun 6, 2009 at 11:25 AM, Jagan Mohano.ja...@gmail.com wrote: Hey

[gmx-users] PME nodes

Dears, I am having troubles finding the better balance between the PME CPUs and the rest. I played with the rdd, rcon and -npme options but nothing really appears very straightforwardly best. I'd appreciate if some of you could post their experience in that matter. I mean the number of

Re: [gmx-users] Reg. g_density

hello Tsjerk, thanks for the reply... the syntax of g_density is such that we need to provide a tpr file right... is there a way of doing it without the tpr... and also from where are the radii of the atoms read for calculation of the volume... or is the volume calculated differently... thanks in

Re: [gmx-users] Reg. g_density

Hi Jagan, I just checked and indeed g_density requires a .tpr file. It would be possible to get an approximate density using a pdb file or so, but that requires hacking the code. For the volume it's the same thing. The radii could be read from the file vdwradii.dat in the GMX library directory

Re: [gmx-users] PME nodes

XAvier Periole wrote: Dears, I am having troubles finding the better balance between the PME CPUs and the rest. I played with the rdd, rcon and -npme options but nothing really appears very straightforwardly best. I'd appreciate if some of you could post their experience in that matter. I

Re: [gmx-users] PME nodes

XAvier Periole wrote: Dears, I am having troubles finding the better balance between the PME CPUs and the rest. I played with the rdd, rcon and -npme options but nothing really appears very straightforwardly best. I'd appreciate if some of you could post their experience in that matter.

Re: [gmx-users] PME nodes

On Jun 6, 2009, at 1:08 PM, Justin A. Lemkul wrote: XAvier Periole wrote: Dears, I am having troubles finding the better balance between the PME CPUs and the rest. I played with the rdd, rcon and -npme options but nothing really appears very straightforwardly best. I'd appreciate if

Re: [gmx-users] PME nodes

XAvier Periole wrote: On Jun 6, 2009, at 1:08 PM, Justin A. Lemkul wrote: XAvier Periole wrote: Dears, I am having troubles finding the better balance between the PME CPUs and the rest. I played with the rdd, rcon and -npme options but nothing really appears very straightforwardly best.

Re: [gmx-users] Scaled 1-5 interactions

* David van der Spoel sp...@xray.bmc.uu.se [2009-06-06 08:06:26 +0200]: Florian Dommert wrote: * Mark Abraham mark.abra...@anu.edu.au [2009-06-05 10:31:22 +1000]: Borys Szefczyk wrote: Dear GROMACS Users, I would like to use the OPLS force field, but with additional scaling factor for the

[gmx-users] g_helix command error

Upon running g_helix_d -s md.tpr -n md.ndx -f md.trr -to gtraj1.g87 -cz zconf1.gro -co waver1.gro -b 0 -e 1000 -dt 1 -w -r0 1 -q -F -db -prop RAD -ev -ahxstart 1 -ahxend 28 I got the following output: Fatal error: rnr==0. Please tell me how can I proceed? Chitrita.

[gmx-users] Nonrepeatable results for gromacs 4.0.5

I've been doing multiple runs using gromacs v 4.0.5 mdrun and a constant topol.tpr input file. Unfortunately, the results that I get in my md.log differ from run to run. For example, Run 1 Started mdrun on node 0 Fri May 22 22:53:51 2009 Step Time Lambda