[gmx-users] compiling gromacs-3.3.1 on itanium2 with icc and ifort

I had trouble compiling gromacs-3.3.1 parallel (but not serial) on itanium2 until I found the following post: http://www.gromacs.org/pipermail/gmx-users/2004-February/009171.html And that solution was good... I now have a functional executable. To clarify, the solution was to do this: export

Re: [gmx-users] Recover velocity from trr file and coordinates from xtc file

You need full precision coordinates (i.e. trr and not xtc) for an accurate restart. You might be able to bodge it with the use of trjconv/trjcat or something to make a "pretend" trr with coordinates and velocities, but I wouldn't count on it. Oh, and a restart file is a tpr, not a gro. Making

Re: [gmx-users] GTP topology file for ffG43a1

Quoting Robert Fenwick <[EMAIL PROTECTED]>: > > Dear all, > > I have now prepared what I think are the necessary lines for entry > into the ffG43a1.rtp file for GTP, however I was wanting a quick way > to test what I have done. Again I am open to suggestions. > Specifically I want to ensure that I

Re: [gmx-users] Re: Problem in atom name correspondence between protein topology and coordinates after mutation grompp

himanshu khandelia wrote: Sorry, there was a little mistake in the reported output of grompp in my previous email. It should be as follows: ## Warning: atom names in protein.top and final.gro don't match (CD2 - HD1) Warning: atom names in protein.top and final.gro don't match

Re: [gmx-users] Double precision test failure

Berk Hess wrote: Ah, this could be the issue. Depending on how you configure the double precision binaries could have the same names as the single precision ones, or they could have _d appended. I guess the test scripts can not figure out what they should use, but currently they apparently reque

[gmx-users] GTP topology file for ffG43a1

Dear all, I have now prepared what I think are the necessary lines for entry into the ffG43a1.rtp file for GTP, however I was wanting a quick way to test what I have done. Again I am open to suggestions. Specifically I want to ensure that I have added sufficient bonds and angles for the

Re: [gmx-users] Writing initial coordinates to trajectory files

Berk Hess wrote: The initial coordinates are written immediately to the trr file, although the file system might buffer data, you so could have to wait until some more frames have been written. Thanks, I see that now. It seems that somewhere between grompp and mdrun's initial trajectory output

Re: [gmx-users] Problem with S-S bond

Hi Tsjerk, Thanks a lot. I tried writing a new message but it was bouncing back to me and I wrote to the administrator, and was suggested to register with GMX,which I already have done. Finally it worked when I replied for a previous message. However, sorry for the inconvenience, it will not

RE: [gmx-users] Writing initial coordinates to trajectory files

I don't understand what it is you want. The initial coordinates are written immediately to the trr file, although the file system might buffer data, you so could have to wait until some more frames have been written. But the initial coordinates are the ones you used to generate the tpr file, so I

Re: [gmx-users] Recover velocity from trr file and coordinates from xtc file

Thank you for your help. However, I can't understand how to generate gro file from trr and xtc files. I'm sorry. I'm a beginner. Would you let me know exact command? or where can I find? Again, I saved *velocity only in trr* file, and I have xtc file (only coordinates). I have edr file also. I f

[gmx-users] Writing initial coordinates to trajectory files

Hello, Is there a setting, or some standard way to write out the initial coordinates of a system to the trajectory file instead of it waiting nstxout steps? Thanks very much, --Brian. PS. I sent this a couple days ago originally - must have gotten lost. Apologies if both make it through. --

Re: [gmx-users] Re: Problem in atom name correspondence between protein topology and coordinates after mutation grompp

Your procedure sounds like it could induce an error in a number of steps. Have you considered simply submitting your initial .pdb file to a program like Sybyl or DeepView and allowing it to make the mutation for you? -Justin Quoting himanshu khandelia <[EMAIL PROTECTED]>: > Sorry, there was a

[gmx-users] Re: Problem in atom name correspondence between protein topology and coordinates after mutation grompp

Sorry, there was a little mistake in the reported output of grompp in my previous email. It should be as follows: ## Warning: atom names in protein.top and final.gro don't match (CD2 - HD1) Warning: atom names in protein.top and final.gro don't match (CE1 - CD2) Warning: atom n

[gmx-users] Problem in atom name correspondence between protein topology and coordinates after mutation grompp

Hi Folks, I am not being able to debug a little problem. I hope someone will be able to point out the mistake. Here is what I am trying to do: I need to mutate a SER to a GLU residue in a protein. However, after mutation (and making a new topology), when I run grompp, I get the following error:

Re: [gmx-users] Double precision test failure

Ah, this could be the issue. Depending on how you configure the double precision binaries could have the same names as the single precision ones, or they could have _d appended. I guess the test scripts can not figure out what they should use, but currently they apparently request the _d appended

Re: [gmx-users] Double precision test failure

The gromacs commands are in my search path as both the commands suggested worked. The single precision tests worked but it was the double precision tests that completely failed. All of the grompp.out files contain the single line error : sh: line 1: grompp_d: command not found Checking the bi

Re: [gmx-users] Replica Exchange MD using Gromacs

Hi Monica, I had not found a detailed tutorial about it; however, you can search for papers in which the simulations are performed via REMD.This will be helpful. Ozge. -Original Message- From: "Monika Sharma" <[EMAIL PROTECTED]> To: gmx-users@gromacs.org Date: Fri, 30 Nov 2007 17:04:07

Re: [gmx-users] rtp file

Hi Justin A. Lemkul , Thank you for your answer.Your answer made me clear suddenly.:)And I think I found the rigth way :) Thank you Özge Kül "Justin A. Lemkul" <[EMAIL PROTECTED]> wrote: Quoting özge kül : > Thank you Justin A. Lemkul for your interest of my question.I looke

[gmx-users] Replica Exchange MD using Gromacs

Dear All, I am trying REMD for the first time using Gromacs. But I am not finding any much helpful material regarding the replica exchange using Gromacs. Can anyone who has done REMD please let me know about any good tutorial where I can understand the way this replica exchange work in gromacs and