RE: [gmx-users] Free energy calculations and speed problems

Hi, Note that there are proper options for this (no cut-off's): ns_type = simple pbc = none nstlist = 0 rlist = 0 rcoulomb = 0 rvdw = 0 Berk. > Date: Tue, 20 May 2008 12:45:35 -0700 > From: [EMAIL PROTECTED] > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] Free energy calculations and spee

Re: [gmx-users] QM/MM compilation

Message: 3 Date: Tue, 20 May 2008 18:59:58 +0200 From: Ran Friedman <[EMAIL PROTECTED]> Subject: Re: [gmx-users] QM/MM compilation To: Discussion list for GROMACS users Message-ID: <[EMAIL PROTECTED]> Content-Type: text/plain; charset=ISO-8859-1 Dear Gerrit, Hitch-hiking with a related issue.

[gmx-users] Invitation to connect on LinkedIn

LinkedIn Discussion, I'd like to add you to my professional network on LinkedIn. -Chandu_Cts Learn more: https://www.linkedin.com/e/isd/271990618/-NzGHjxY/ -- What is LinkedIn? Maintain and develop your professional network: Like Cha

[gmx-users] Water molecule can not be settled

Hi, My simulation has fall over with this error: t = 501.346 ps: Water molecule starting at atom 8367 can not be settled. Check for bad contacts and/or reduce the timestep.Wrote pdb files with previous and current coordinates What can I do to fix it? There are a few other that have had this

[gmx-users] how to edit pdb file

Dear GMX users, I have a basic question. I want to put two same box in x direction. So I need increase the number of atoms and change their x coordinates,then combine it with the original one. But the file created by Excel can't be recoganized by gromacs. Is there any method in Gromacs

Re: [gmx-users] how to edit pdb file

Hi, have look to this: http://stein.bioch.dundee.ac.uk/~charlie/software/pdb-mode/pdb-mode.html I found it very useful regards andrea Wei, Xiupeng wrote: > Dear GMX users, > I have a basic question. I want to put two same box in x direction. > So I need increase the number of atoms a

Re: [gmx-users] how to edit pdb file

Copy file, editconf to translate, then concatenate that with the original, reorder and renumber everything; or genbox will also do something similar with less tinkering. - Original Message From: "Wei, Xiupeng" <[EMAIL PROTECTED]> To: "gmx-users@gromacs.org" Sent: Wednesday, May 21, 200

Re: [gmx-users] how to edit pdb file

Quoting "Wei, Xiupeng" <[EMAIL PROTECTED]>: > Dear GMX users, > I have a basic question. I want to put two same box in x direction. > So I need increase the number of atoms and change their x coordinates,then > combine it with the original one. But the file created by Excel can't be > rec

Re: [gmx-users] how to edit pdb file

Hi, Andrea As Xiupeng is on th side of using proprietory software, Xemacs would definitely be an overdose. Hi, Xiupeng All you need is to know is basic PDB file format. ATOM records in PDB file is in fixed-width column format. You need to format your line according to what said here. http://

[gmx-users] problem with genion (gromacs 3.3.99)

Hi all, I do have a weird behaviour with genion, which fails with the message: ftp2fn: No filetype .??? No option -cpo Segmentation fault and I can't figure out what I do wrong. I couldn't not find any reference to it either. It seems that a file cannot be accessed but I couldn't get in wh

Re: [gmx-users] Water molecule can not be settled

Robert Fenwick wrote: Hi, My simulation has fall over with this error: t = 501.346 ps: Water molecule starting at atom 8367 can not be settled. Check for bad contacts and/or reduce the timestep.Wrote pdb files with previous and current coordinates What can I do to fix it? There are a few ot

[gmx-users] cannot print velocity information to trr/xtc files (Carbon Naotube inside water)

Dear all, I am doing a simulation of a carbon nanotube (CNT) inside water. First I am going to describe my problem and then give info about my simulation setup (initial conditions, parameters, etc.). My problem is as follows: (1) I am doing a *.gro file of a *.pdb of a (16,16) CNT, without usi

[gmx-users] QM/MM between Gromacs and Gamess-US

Dear Gromacs Users, I am wondering if a QM/MM interface between Gromacs and Gamess-US has already been available, or it will be available in the upcoming Gromacs_4? I know that Gromacs_3 has an interface for Gamess-UK, which is unfortunately not free for users outside UK. Thanks. Hanning

[gmx-users] how to remd analysi?

Dear all users: I performed remd using GROMACS 3.3.1,but I find that I do not know how to analyze the result further,though I have demux.pl script and produced replica_index.xvg and replica_temp.xvg files, the contents of two files are the same! I use trjcat_d to produce a continuous trajector

Re: [gmx-users] cannot print velocity information to trr/xtc files (Carbon Naotube inside water)

Quoting CIHAN NADIR KAPLAN <[EMAIL PROTECTED]>: > Dear all, > > I am doing a simulation of a carbon nanotube (CNT) inside water. First I am > going to describe my problem and then give info about my simulation setup > (initial conditions, parameters, etc.). > > My problem is as follows: > > (1) I

Re: [gmx-users] cannot print velocity information to trr/xtc files (Carbon Naotube inside water)

CIHAN NADIR KAPLAN wrote: Dear all, I am doing a simulation of a carbon nanotube (CNT) inside water. First I am going to describe my problem and then give info about my simulation setup (initial conditions, parameters, etc.). My problem is as follows: (1) I am doing a *.gro file of a *.pdb of

Re: [gmx-users] how to remd analysi?

xi zhao wrote: > Dear all users: > I performed remd using GROMACS 3.3.1,but I find that I do not know how > to analyze the result further, "Analyze" really doesn't tell us what you're trying to do. > though I have demux.pl script and produced > replica_index.xvg and replica_temp.xvg files, the

[gmx-users] about DMSO c-c bond and c-o bond in ffg53a6 force field

Hi, everyone. I am simulating DMSO. At fisrst ,bond parameters contain two c-c bonds,and c-o bond ,which actually not in existence. But gmx 's force field ffg53a6 documents in top directory defines these bonds. When running mdrun , system reminds "segmentation default". then i get these virtual bo

[gmx-users] .trr file

Hi all, I am quite new to Gromacs and would like to ask why the full _restart_ file .trr is designed such that every frame's coordinates and velocities are retained? In NAMD and Amber only the last frame's coordinates and velocities are necessary for a restart. I mention this because am wo

Re: [gmx-users] .trr file

Low Soo Mei wrote: Hi all, I am quite new to Gromacs and would like to ask why the full _restart_ file .trr is designed such that every frame's coordinates and velocities are retained? It only does this if you choose to do this. See discussion here http://wiki.gromacs.org/index.php/Doing_

Re: [gmx-users] .trr file

Low Soo Mei wrote: Hi all, I am quite new to Gromacs and would like to ask why the full _restart_ file .trr is designed such that every frame's coordinates and velocities are retained? In NAMD and Amber only the last frame's coordinates and velocities are necessary for a restart. I mention

回复： Re: [gmx-users] how to remd ana lysi?

I performed remd using GROMACS 3.3.1 at four different temperatures: 270k, 400k, 540k, 660k, and produced four trajectories. I want to know whether my simulation is ok, but I do not know how to analysis my trajectories. Though I have demux.pl script and produced replica_index.xvg and replica_te

Re: 回复： Re: [gmx-users] how to remd an alysi?

xi zhao wrote: > I performed remd using GROMACS 3.3.1 at four different temperatures: > 270k, 400k, 540k, 660k, and produced four trajectories. I want to know > whether my simulation is ok, but I do not know how to analysis my > trajectories. Though I have demux.pl script and produced > replic

[gmx-users] which code should I rewrite the function of "position restraints"?

Dear GROMCS users: I found the following past discussions in the gmx-users ML. [gmx-users] simulations using structureless surface-2 Mark Abraham mark.abraham at anu.edu.au Fri Jul 27 01:56:17 CEST 2007 --- > Dear gmx users, > my apologies

Re: [gmx-users] which code should I rewrite the function of "position restraints"?

Makoto Yoneya wrote: Dear GROMCS users: I found the following past discussions in the gmx-users ML. [gmx-users] simulations using structureless surface-2 Mark Abraham mark.abraham at anu.edu.au Fri Jul 27 01:56:17 CEST 2007 --- Dear gmx