[gmx-users] Use different fudgeLJ and fudgeQQ values in simulations with the AMBER force field

Dear gmx users, Recently I have parametrized a new force field for glycolipid molecules based on the GLYCAM parameters. I would like to use it with the AMBER99SB-ILDN force field in gromacs for simulations of peptides and glycolipds. As you know GLYCAM uses two different values for fudgeLJ and

[gmx-users] [Fwd: g_sas for each residu]

Hi all, I would like to use g_sas to compute and give surface area changes of each residu of a peptide (25 AA long) and *not* the average per residu given by the argument -or) along the simulation time. If yes how ? Of course, i think, i can use an index file, but for 25 AA, it will take a

[gmx-users] Re: gmx-users Digest, Vol 79, Issue 124

OK thank you all, I give up :-( a bientot Stephane Abel wrote: OK thank you for your help justin With the change you have suggested, grompp starts but an other error come quickly with the first line of the gb.itp: ERROR 1 [file /home/cont003/abel01/charmm27.ff//gb.itp, line 1

[gmx-users] Use an altenative folder for itp files

uggestion ? Stefane -- Message: 3 Date: Wed, 17 Nov 2010 07:59:20 -0500 From: "Justin A. Lemkul" Subject: Re: [gmx-users] [Fwd: Use an altenative folder for itp files] To: Discussion list for GROMACS users Message-ID: <4ce3d1a8.9070...@vt.edu> Content-Type: text/plain; charset=ISO-8859-1;

[gmx-users] [Fwd: Use an altenative folder for itp files]

Dear all, I have a little question about the use of a alternative localization of the ff librairy in GMX4.0.7. These (old) version of GMX is installed in a big cluster and i would like to use it for testing some CHARMM27 parameters. Since the charmm27.ff is not given this distribution, i wo

[gmx-users] CHARMM TIP3-Water with GMX

Hi all I am doing some tests with the CHARMM port in GROMACS. Before to start more extensive simulations with this ff I have performed a short run of 1000 TIP3-CHARMM water molecules in a cubic during at T=300 K and P=1.015 bar with v-rescale and PR as thermostat and barostat. I have used the

[gmx-users] Re: Obtain a pre-version of gromacs 4.1 without git

Thank you Roland for your response I have effectively downloaded from the http://repo.or.cz/w/gromacs.git/snapshot/HEAD.tar.gz, the HEAD version of gmx Unfortunately, the unpacked directory does not contain a configure file, I have only an configure.ac. So my question is: how to obtain a ful

[gmx-users] good Atom type in gromacs with the AMBER ff

Ok ! Thank you everybody for your help Stephane Message: 3 Date: Wed, 30 Sep 2009 19:36:26 -0400 From: "Justin A. Lemkul" Subject: Re: [gmx-users] good Atom type in gromacs with the AMBER ff port To: Discussion list for GROMACS users Message-ID: <4ac3eb7a.6020...@vt.edu> Content-Type:

[gmx-users] Problem with domain decomposition

Hi gromacs users and experts I am doing some simulations using 8 CPU of solvate peptide (8 AA) in octahedron truncated box (5150) with SPC water with GMX 4.05. To simulate during a long time i am cutting my simulation in 24 h time period (25 ns/day) using checkpoints. During my last simu

[gmx-users] Large fluctuation of protein temperature with nose hoover thermostat

Hi gromacs experts, For my simulations of peptide (8 AA) in water (5100, SPC/E) and with 1 Cl- i use the Nose-Hoover Thermostat to simulate in NVT ensemble. Since i am a beginner with GROMACS, i have a question with the tau_t parameters Parameters i used I ; Temperature coupling is on tcoupl

[gmx-users] Continuation a run with checkpoint issue

Hi gromacs users I would like to continue a run up 3000 ps (with a preceding MD performed during a 1ns) on a cluser with 8 CPU Here the commands i used Run 1: during 1 ns in NVT ensemble grompp_mpi -f md.mdp -c nvt.gro -t npt.trr -p topol.top -o md_0_1.tpr /usr/pbs/bin/mpiexec /scratch/taul

[gmx-users] Re: Add acetyl and amide caps to a peptide with pdb2gmx

Hi Justin, I have resolved problem: A typo for the NH2 cap dihedral parameters in ff53a6.rtp file (as you indicate in your tutorial). Thank you Stef. gmx-users-requ...@gromacs.org wrote: Send gmx-users mailing list submissions to gmx-users@gromacs.org To subscribe or unsubs

[gmx-users] Add a amide and acetylated caps to a peptide with pdb2gmx

Hi all I would like to add to a peptide two caps in N and C term for subsequent simulations with GMX(v4.05) with the ffG53a6 ff. For this purpose i added manually the the missing atoms in my pdb file taken from the pdb databank and rename the residus ACE and NH2 ATOM 1 C ACE A 145

[gmx-users] Add acetyl and amide caps to a peptide with pdb2gmx

Hi gromacs users I would like to add a acetyl and amide caps (N and C term) to a peptide for subsequent simulations with with GMX(v4.05) and the ffG53a6 ff . For this purpose i have added manually the missing atoms in my pdb files taken from the protein databank My pdb file has the following

[gmx-users] Membrane protein tutorial

gmx-users-requ...@gromacs.org wrote: Send gmx-users mailing list submissions to gmx-users@gromacs.org To subscribe or unsubscribe via the World Wide Web, visit http://www.gromacs.org/mailman/listinfo/gmx-users or, via email, send a message with subject or body 'help' to