Re: [gmx-users] how to use demux.pl for REMD analysis

Mark Abraham wrote: N-J.M. Macaluso wrote: Hello, I've been reading all of the archived questions on the analysis of REMD in Gromacs, and I'm still a bit confused. It appears that the first step is to use the demux.pl script to demultiplex the REMD trajectories. How to use this script, a

RE: [gmx-users] Parameterizing a force field

Not sure if this is what you want, but the -j and -jo switches with mdrun allow you to run a simulation and vary some of the parameters for forcefield parameterisation. Catch ya, Dr. Dallas Warren Lecturer Department of Pharmaceutical Biology and Pharmacology Victorian College of Pharmacy, Monash

Re: [gmx-users] Parameterizing a force field

Lee-Ping wrote: Hi there, I'd like to fit a set of force field parameters (100+) to a set of several ab initio force calculations. I've noticed that ffscan is tailored to this purpose, but I don't know how to use it, so I wrote a script that tries to fit the force field parameters using some nu

Re: [gmx-users] Positive and negative ions move in the same direction under a constant electric field?

Tom Weingarten wrote: > I'm not sure if this has been addressed previously, but perhaps the > reason why we're seeing so many users performing incorrect temperature > coupling of ions is because that is how it is done in the very popular > fwspider tutorial. In fact this tutorial is the first hi

Re: [gmx-users] how to use demux.pl for REMD analysis

N-J.M. Macaluso wrote: Hello, I've been reading all of the archived questions on the analysis of REMD in Gromacs, and I'm still a bit confused. It appears that the first step is to use the demux.pl script to demultiplex the REMD trajectories. How to use this script, and what exactly this

Re: [gmx-users] Problems using grompp and amber force field

Hi, Thanks everybody by the comments. There was a error in the include files of the topology: The itp file generated by pdb2gmx program was localized in a different folder that where we were running to the grompp program. Mario El mar, 08-05-2007 a las 02:05 +0100, TJ Piggot escribió: > Hi, > >

[gmx-users] Parameterizing a force field

Hi there, I'd like to fit a set of force field parameters (100+) to a set of several ab initio force calculations. I've noticed that ffscan is tailored to this purpose, but I don't know how to use it, so I wrote a script that tries to fit the force field parameters using some numerical optimizati

Re: [gmx-users] Very large fluctuations in dg/dl

Hi John and David, I reply to you both. Thank you very much for your complete answers as well as for all the pointers you mentioned. I will have a look at these references. Free energy calculation is definitely a challenging issue ! Cheers, Patrick John D. Chodera a écrit : Hi Patrick, I li

Re: [gmx-users] Very large fluctuations in dg/dl

Hi Stephane, just to finish with this story, I took the value 54 determined in (Hunenberger & van Gunsteren,1998,J Chem Phys; Smith & van Gunsteren, 1994, J Chem Phys), that has been updated to 61 since then. But as stated by Berk and Lars it will hardly make any difference in the properties I

[gmx-users] cosine content

Dear users, I am trying to calculate cosine content of the principal components using g_analyze. I am using time versus projection of trajectory along eigenvector 1 (extracted from proj.xvg of g_anaeig) as an input file for g_analyze. When I calculated the same for eigenvector 2, got memory alloc

Re: [gmx-users] Positive and negative ions move in the same direction under a constant electric field?

I'm not sure if this has been addressed previously, but perhaps the reason why we're seeing so many users performing incorrect temperature coupling of ions is because that is how it is done in the very popular fwspider tutorial. In fact this tutorial is the first hit on google for "gromacs tutoria

[gmx-users] how to use demux.pl for REMD analysis

Hello, I've been reading all of the archived questions on the analysis of REMD in Gromacs, and I'm still a bit confused. It appears that the first step is to use the demux.pl script to demultiplex the REMD trajectories. How to use this script, and what exactly this is supposed to accomplis

Re: [gmx-users] eigenvectors in eigenvec.trr file

Hi Sunita, Didn't you have a t=-1 for the reference structure? At least I think that the reference structure will account for the additional vector. Cheers, Tsjerk On 5/9/07, [EMAIL PROTECTED] <[EMAIL PROTECTED]> wrote: Dear Users, Covarience analysis is performed on Calpha atoms of the pept

[gmx-users] nst option in g_cluster seems to be not working

Dear users, g_cluster has an option 'nst' to write clusters when the no. of members are more than specified number. It seems that the option is not working. How should I proceed if I want to perform the same? With regards, Sunita ___ gmx-users mailin

Re: [gmx-users] Trjconv: reducing frames and Time issue

Hi, What Alan refers to is the following: -timestep time 0 Change time step between input frames (ps) which you could have read from the manual/manpage/help on trjconv. With timestep you change the time step between the frames (to 20ps), skipping 2 frames, makes 40ps timesteps in your o

Re: [gmx-users] charge

Hi, I wish to simulate a ligand-protein system..I have used the prodrg server to create the .itp file for my ligand. I have done gaussian charge calculation for my ligand using the chelpg method. how should i incorporate the gaussian charges into my .itp file. should i copy the charges for hea

[gmx-users] charge

Hi, I wish to simulate a ligand-protein system..I have used the prodrg server to create the .itp file for my ligand. I have done gaussian charge calculation for my ligand using the chelpg method. how should i incorporate the gaussian charges into my .itp file. should i copy the charges for heavy

[gmx-users] Parameter QMcharge does not work with Gromacs-CPMD

Hi. It seems as if the "QMcharge"-Parameter of Gromacs is not used in Gromacs-CPMD. The CPMD_inp.run should be expanded by the lines: CHARGE [charge in 'e'] in the &SYSTEM paragraph if "QMcharge" is used in the Gromacs Input-File. With regards Christian Seifert.

Re: [gmx-users] Very large fluctuations in dg/dl

Stéphane Téletchéa wrote: Patrick Fuchs a écrit : Hi Gromacs users, I have a few questions related to solvation free energy calculation via thermodynamic integration. #ifdef FLEX_SPC #include "flexspc.itp" #else #include "spc.itp" #endif coulombtype= generalized-reaction-fi

Re: [gmx-users] Very large fluctuations in dg/dl

From: Stéphane Téletchéa <[EMAIL PROTECTED]> Reply-To: Discussion list for GROMACS users To: Discussion list for GROMACS users Subject: Re: [gmx-users] Very large fluctuations in dg/dl Date: Wed, 09 May 2007 11:11:06 +0200 Patrick Fuchs a écrit : Hi Gromacs users, I have a few questions re

[gmx-users] eigenvectors in eigenvec.trr file

Dear Users, Covarience analysis is performed on Calpha atoms of the peptide simulation. g_covar writes eigenvectors to a trajectory file (eigenvec.trr).I converted this file into readable format by using gmxdump.It gives the eigenvectors with eigenvector number as timestamp. t=0 corresponds to ave

Re: [gmx-users] change the ligand in pdb file

Hi, On Wednesday, 9. May 2007 10:45, Rui Li wrote: > Dear all, > I want to change the ligand in pdb file(add,delete atoms and change > conformation),Who can introduce a software to me? > Any reply is appreciated.Thanks in advance As Erik said pymol is a possible solution, but i don`t think th

Re: [gmx-users] Very large fluctuations in dg/dl

Patrick Fuchs a écrit : Hi Gromacs users, I have a few questions related to solvation free energy calculation via thermodynamic integration. #ifdef FLEX_SPC #include "flexspc.itp" #else #include "spc.itp" #endif coulombtype= generalized-reaction-field rcoulomb = 1.

Re: [gmx-users] change the ligand in pdb file

Try Pymol. I've never used it for such editing, but it seems to be capable of if. /Erik 9 maj 2007 kl. 10.45 skrev Rui Li: Dear all, I want to change the ligand in pdb file(add,delete atoms and change conformation),Who can introduce a software to me? Any reply is appreciated.Thanks i

[gmx-users] change the ligand in pdb file

Dear all, I want to change the ligand in pdb file(add,delete atoms and change conformation),Who can introduce a software to me? Any reply is appreciated.Thanks in advance ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/m

Re: [gmx-users] Human Serum Albumin problem

Hi, On Wednesday, 9. May 2007 02:20, George Abadir wrote: > Hi, > I have downloaded the 1HA2.pdb (describing human serum albumin) > file from www.pdb.org and ran pdb2gmx to make a topology file for it. I > got an error message "Source code file: hizzie.c, line: 267 > Fatal error: Incomplete r

Re: [gmx-users] Human Serum Albumin problem

Hi George, you should read the publication carefully. Also in the pdb file it says that there are missing residues and missing atoms in some residues (eg HIS3). As mentioned many times in the list, you should not use the -missing option unless you want to simulate broken system (usually you d