[gmx-users] rdf range

2011-01-29 Thread Thomas Koller
Hello! One question: I want to plot the rdf functions. How can I adjust to fix how far the rdf is plotted over the distance? I want to see the rdfs over long distance r. Where can I adjust that? Thanks! Thomas -- Empfehlen Sie GMX DSL Ihren Freunden und Bekannten und wir belohnen Sie mit bis

Re: [gmx-users] Simulation time losses with REMD

2011-01-29 Thread Mark Abraham
On 28/01/2011 4:46 PM, Mark Abraham wrote: Hi, I compared the .log file time accounting for same .tpr file run alone in serial or as part of an REMD simulation (with each replica on a single proessor). It ran about 5-10% slower in the latter. The effect was a bit larger when comparing the sam

[gmx-users] Missing Amino Acids

2011-01-29 Thread simon sham
Hi, 1. I have a protein which is missing both the first and last amino acids in the sequence. Do you know any free linux softwares that can insert these missing amino acids? 2. Since only two amino acids are missing, one in both end, can I simply ignore them in simulations? Thanks for your insi

Re: [gmx-users] Missing Amino Acids

2011-01-29 Thread Justin A. Lemkul
simon sham wrote: Hi, 1. I have a protein which is missing both the first and last amino acids in the sequence. Do you know any free linux softwares that can insert these missing amino acids? A number of possibilities are listed here: http://www.gromacs.org/Documentation/File_Formats/Coord

Re: [gmx-users] mdrun with append option

2011-01-29 Thread Sai Pooja
I would be happy to supply more information.. if someone could please look into this.. otherwise I will have to switch to storing every file and then just concatenating them which seems like a rather roundabout way of doing it. On Fri, Jan 28, 2011 at 4:37 PM, Sai Pooja wrote: > This is the comm

Re: [gmx-users] mdrun with append option

2011-01-29 Thread Justin A. Lemkul
Sai Pooja wrote: I would be happy to supply more information.. if someone could please look into this.. otherwise I will have to switch to storing every file and then just concatenating them which seems like a rather roundabout way of doing it. In theory, there's nothing wrong with what y

Re: [gmx-users] mdrun with append option

2011-01-29 Thread Justin A. Lemkul
Disregard the version question; I see it now in the command string. You should still check for errors, and consider using version 4.5.3 to see if the issue persists. -Justin Justin A. Lemkul wrote: Sai Pooja wrote: I would be happy to supply more information.. if someone could please lo

Re: [gmx-users] mdrun with append option

2011-01-29 Thread Mark Abraham
On 30/01/2011 10:39 AM, Sai Pooja wrote: I would be happy to supply more information.. if someone could please look into this.. otherwise I will have to switch to storing every file and then just concatenating them which seems like a rather roundabout way of doing it. As I suggested a few ema

RE: [gmx-users] Simulation time losses with REMD

2011-01-29 Thread martyn.winn
> -Original Message- > From: gmx-users-boun...@gromacs.org [mailto:gmx-users- > boun...@gromacs.org] On Behalf Of Mark Abraham > Sent: 29 January 2011 08:24 > To: Discussion list for GROMACS users > Subject: Re: [gmx-users] Simulation time losses with REMD > > On 28/01/2011 4:46 PM, Mark

Re: [gmx-users] Simulation time losses with REMD

2011-01-29 Thread Mark Abraham
On 30/01/2011 10:26 AM, martyn.w...@stfc.ac.uk wrote: -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users- boun...@gromacs.org] On Behalf Of Mark Abraham Sent: 29 January 2011 08:24 To: Discussion list for GROMACS users Subject: Re: [gmx-users] Simulation time losse