[gmx-users] Configurations stored in REMD trajectories

Dear all, perhaps someone can help me with this doubt. When a REMD simulation is run, which configuration is stored for any given replica, the one before the exchange or the one that we get after the exchange (i.e. the exchange partner configuration)? Best regards Cesar -- gmx-users mailing list

Re: [gmx-users] Configurations stored in REMD trajectories

Thanks :D 2011/12/30 Mark Abraham mark.abra...@anu.edu.au On 31/12/2011 7:03 AM, César Ávila wrote: Dear all, perhaps someone can help me with this doubt. When a REMD simulation is run, which configuration is stored for any given replica, the one before the exchange or the one that we get

[gmx-users] Reproducing Chain Tilt on DPPC gel phase with Martini FF

Dear all, I would like to simulate a DPPC membrane in gel phase using Martini Force Field. As stated on Simulation of gel phase formation and melting in lipid bilayers using a coarse grained model, CPL 135 (2005) 223-244 the correct 30º angle chain tilt for DPPC might be reproduced by reducing

Re: [gmx-users] How can I reconstruct the system in CGMD simulation?

I suggest you read the original paper for Martini Protein FF. I think it is not suitable for your purpouse. 2009/12/17 rasoul nasiri nasiri1...@gmail.com Hi, My purpose is finding of denaturation mechanism of proteins with MArtini CGFF by Gromacs. I mean after filling box in which there are

Re: [gmx-users] How can I reconstruct the system in CGMD simulation?

in CGMD simulation or I have to reconstruct the system in smaller vdw distance of the water beads for doing my purpose. and Which commands of Gromacs can do it? Best regards Rasoul On Thu, Dec 17, 2009 at 5:03 PM, César Ávila clav...@gmail.com wrote: I suggest you read the original paper

Re: [gmx-users] do we still have a do_dssp and dssp compatibility issue? thread: do_dssp failed to execute

I was dealing with the same situation. I am using the latest version of DSSP (April 2011). Neither gromacs 4.5.3 or 4.5.4 would work. After applying Pradip's patch, do_dssp worked for me. I would say that the change in flags is related to the fact that In 2011 Maarten Hekkelman has written new

[gmx-users] git release-4-5-patches behind proxy

I want to calculate secondary structure propensities of residues. Following Mark's message on thread Re: [gmx-users] secondary structure propensities of residues I would like to get the release-4.5-patches from git (in order to get do_dssp.c). Nevertheless I found problems while trying to fetch

Re: [gmx-users] secondary structure propensities of residues

Hi, I downloaded release-4-5-patches from git. It compiles and installs successfully. Nevertheless I am getting a segmentation fault. With gdb I am getting the following messages gdb --args do_dssp -f ../0_trajout.xtc -s ../input/replica_0.tpr -ssdump data.dat -b 17 -e 18 -dt 10 GNU gdb

Re: [gmx-users] secondary structure propensities of residues

I am using the latest vesion of DSSP (the one available at DSSP homepage) 2011/8/11 Mark Abraham mark.abra...@anu.edu.au On 10/08/2011 6:03 AM, César Ávila wrote: Hi, I downloaded release-4-5-patches from git. It compiles and installs successfully. Nevertheless I am getting a segmentation

[gmx-users] Replex in REMD

Dear all, I am running REMD simulations in gromacs. Taking advantage of vsites I have set the timestep to 5 fs. In the mdp file I have adjusted the energy and frames to be written every 1000 steps (5 ps). While running the simulations I have also selected the exchange trials to be done every 1000

[gmx-users] CMAP for alanine dipeptide in Charmm27 ff

I would like to run REMD simulations on the alanine dipeptide using the Charmm27ff + CMAP. Still, after processing the pdb with pdb2gmx, I do not see any entrance referring to the cmap term in the topology file. Does this mean that Cmap won't be calculated? -- gmx-users mailing list

[gmx-users] Re: CMAP for alanine dipeptide in Charmm27 ff

It looks like pdb2gmx does not generate an entrance for cmap terms. I added it manually to the topology file. 2011/10/8 César Ávila clav...@gmail.com I would like to run REMD simulations on the alanine dipeptide using the Charmm27ff + CMAP. Still, after processing the pdb with pdb2gmx, I do

Re: [gmx-users] CMAP for alanine dipeptide in Charmm27 ff

are you using? cMAP is implemented in v4.5 or later Jianguo -- *From:* César Ávila clav...@gmail.com *To:* Discussion list for GROMACS users gmx-users@gromacs.org *Sent:* Sunday, 9 October 2011 12:07 AM *Subject:* [gmx-users] CMAP for alanine dipeptide in Charmm27 ff

Re: [gmx-users] CMAP for alanine dipeptide in Charmm27 ff

Done 2011/10/10 Mark Abraham mark.abra...@anu.edu.au On 11/10/2011 4:51 AM, César Ávila wrote: v4.5.4 As I commented above, I had to manually add an entrance for the cmap terms in the topology file as pdb2gmx would not generate them for the alanine dipeptide. There seems to be no problem

[gmx-users] Using Charmm FF with implicit solvent on gromacs

Dear all, I would like to know if anyone has experience on running simulations using the Charmm FF and implicit solvent model on gromacs. I have found that gromacs has three implementations for GB models - Still - Hawkins-Cramer-Truhlar (HCT) - Onufriev-Bashford-Case (OBC) The charmm FF

[gmx-users] Adding custom residue to Charmm FF in Gromacs

Hi, I would like to add topology and parameter information for a custom residue to the CHARMM forcefield on GROMACS 4.5.3. Which are the files that I should edit for this? Should I also perform some units conversion? Thanks Cesar -- gmx-users mailing listgmx-users@gromacs.org

Re: [gmx-users] Thermostat for REMD simulations in implicit solvent

-1. This means you should set tau-t = 0.0109 rather than 91. Try this and see if the problem goes away! /Per 26 nov 2010 kl. 15:55 skrev César Ávila clav...@gmail.com: Dear all, I am trying to set up a REMD simulation for a peptide (CHARMM ff) in implicit solvent (OBC GB). Following