[gmx-users] hi

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[gmx-users] Hi

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RE: [gmx-users] AFM pulling simulations

rce in that direction). > Date: Tue, 22 Mar 2011 11:15:54 -0400 > From: jalem...@vt.edu > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] AFM pulling simulations > > > > X Rules wrote: > > Hello All, > > > > I am looking for a very

RE: [gmx-users] AFM pulling simulations

ter apply the force in that direction). > Date: Tue, 22 Mar 2011 11:15:54 -0400 > From: jalem...@vt.edu > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] AFM pulling simulations > > > > X Rules wrote: > > Hello All, > > > > I am looking for a very

[gmx-users] AFM pulling simulations

Hello All, I am looking for a very simple (step-by-step) tutorial on AFM pulling simulations (constant force/ constant velocity) with gromacs. Can someone point me to a simple tutorial to perform these simulations with gromacs? Thanks, -- gmx-us

RE: [gmx-users] disparity in RMSD calculation

I have had a similar experience, I have not investigated it thoroughly at the moment, but I get different (identical with specific jumps possibly due to pbc) plots if I take starting structure as my input pdb file or if my starting structure is first structure of trajectory. I think the plots

RE: [gmx-users] mpdboot and mpirun hangs (not crashing)

I am trying to check some of these issues. thanks for your help Date: Sat, 20 Nov 2010 03:38:08 +1100 From: mark.abra...@anu.edu.au To: gmx-users@gromacs.org Subject: Re: [gmx-users] mpdboot and mpirun hangs (not crashing) Message body On 20/11/2010 2:57 AM, X Rules

[gmx-users] mpdboot and mpirun hangs (not crashing)

Hi, I am trying to run my production run with mpirun and this hangs (basically stop writing any files). The processes continue to run without any output. I have to kill and restart which again hangs after some time. Does anyone have any problems with this? what I am doing is mpdboot -n

RE: [gmx-users] Error on Box Length when adding ions (gromacs 4.5.3/Charmm27/Tip3p)

> > There was a bug in an early 4.0.x feature that box vectors were not properly > written to .pdb files (CRYST line), but this was obviously fixed months, if > not > a year or more, ago. Gromacs tools are expected to handle numerous file > types > effortlessly, so using .gro is certainly

RE: [gmx-users] Error on Box Length when adding ions (gromacs 4.5.3/Charmm27/Tip3p)

> The error would imply that the box you have set up is < 2.0 nm, given the > cutoffs here. How did you define the box (editconf command)? What is your > box > size (last line of the .gro file or in the header of a .pdb)? > > -Justin okey.. I got it under control. The problem was. 1. crea

[gmx-users] Error on Box Length when adding ions (gromacs 4.5.3/Charmm27/Tip3p)

= xyz ; Periodic Boundary Conditions (yes/no) Hope you can locate my error here!! > Date: Wed, 17 Nov 2010 13:09:32 -0500 > From: jalem...@vt.edu > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] Error on Box Length when adding ions (gromacs > 4.5.3/

[gmx-users] Error on Box Length when adding ions (gromacs 4.5.3/Charmm27/Tip3p)

I am having problems with grompp with my system. I am using Gromacs 4.5.3 FF = Charmm27 beta WT = TIP3P (recommended and its claimed its not too different than Charmms TIP3P) during minimization with pbc, I get the error about box length being small if I add neutralizing ions (I do not get t

RE: [gmx-users] Problem in setup energy minimization step(grompp)

> Date: Mon, 26 Jul 2010 07:26:04 -0400 > From: jalem...@vt.edu > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] Problem in setup energy minimization step(grompp) > > > > X Rules wrote: > > Precisely, > > > > open your xyz.top file and

RE: [gmx-users] Problem in setup energy minimization step(grompp)

Precisely, open your xyz.top file and search for #include "spc.itp" and replace this line with #include "tip4p.itp" and you will be done with. > Date: Mon, 26 Jul 2010 07:00:57 -0400 > From: jalem...@vt.edu > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] Problem in setup energy mini

RE: [gmx-users] Fatal error: No such moleculetype Cl

Okey, I found the solution, it is the IFDEF statements in ions.itp. OPLS does not have CL but a CL- and therefore when I changed to CL- in my $FILE.top, it went through smoothly. Cheers, From: xru...@live.com To: gmx-users@gromacs.org Date: Mon, 26 Jul 2010 06:58:57 + Subject: [gmx-users]