[gmx-users] free energy landscape question

Hi, I am trying to use g_sham to obtain free energy landscape from a simulation. I can obtain the .xpm files but I want to know if there is any way of obtaining the actual histogram (in a form of a ASCII matrix vith numerical values) to use it in some other plotting program to draw contour lines p

Re: [gmx-users] umbrella sampling-Bimodal Histograms

I took initial 300 as equilibration,Now it seems fine. Thank you .. On Tue, Jun 22, 2010 at 9:21 AM, wrote: > Take that replica on the left that shows a bimodal histogram. Now plot a > time series of the displacement: x-axis = time and y-axis = displacement > along reaction coord. Is it jumping

[gmx-users] fcstep value for shell particles

Dear all, I am trying to perform a simulation with polarizable model using Drude shell particle approach. What should be the optimum value of fcstep if my shell particle has zero mass? As far as I can understand, the default value for fcstep is 0, but can't understand what does it mean from

RE: [gmx-users] fcstep value for shell particles

Hi, fcstep is only relevant for flexible constraints (hence the fc in the step). It does not affect shells. Berk From: mstu...@slb.com To: gmx-users@gromacs.org Date: Tue, 22 Jun 2010 12:25:29 +0200 Subject: [gmx-users] fcstep value for shell particles Dear all, I am trying

[gmx-users] dgdl.xvg file

Hi, Is there command in .mdp to adjust of frequency to write dg/dlamda to dGdL.xvg file? I do mdrun for 100 steps, so I get 100 dg/dl in dgdl.xvg file while I want to change output to write 1000 dgdl in dGdL.xvg file. How can I do? thaks in advance, Afsaneh Maleki -- gmx-users mailing

[gmx-users] OPLS-AA topologies for ATP

Hi, Does anyone have OPLS-AA topologies for ATP? Thanks, Efrat-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Us

[gmx-users] problem while removing extra waters from a simulation box, simulation explodes thereafter

Hi I have run a lipid bilayer simulation, which has too much water in it and too few lipids (small bilayer patch, ~ 80 waters per lipid). I have used genconf to multiply the system in the xy direction to increase system size, and then removed water which is z<8 angstroms and z>92 angstroms using v

[gmx-users] RE:Multiple chain ID's

Hello again, I am still working on gromacs sims on the side of wet lab work. In any case, I am still at the same point as almost several weeks back. I can take my pdb file with 5 chain IDs A-C and generate a .top and .gro file, with appropriate box (which can just be pasted at the top of the

Re: [gmx-users] RE:Multiple chain ID's

lloyd riggs wrote: Hello again, I am still working on gromacs sims on the side of wet lab work. In any case, I am still at the same point as almost several weeks back. I can take my pdb file with 5 chain IDs A-C and generate a .top and .gro file, with appropriate box (which can just be paste

[gmx-users] standard state correction of delta G from a PMF

Hello. I was wondering if anyone could explain how to convert delta G's from a PMF (generated by umbrella sampling and WHAM) into standard state values? There are some posts here on how to do this, but are too mathematical for me to figure out. I also found the same problem when reading some pap

[gmx-users] error in parallel mdrun

Hi all I have a ran a simulation of 64 molecules in a cubic box with side 6 nm, using nose-hoover thermostat, parinello-rahman pressure coupling, and pme. Runnin the simulation in parallel is no problem (using 16 CPUs). However when I want to run an almost identical molecule using the exact same c

Re: [gmx-users] error in parallel mdrun

Gavin Melaugh wrote: Hi all I have a ran a simulation of 64 molecules in a cubic box with side 6 nm, using nose-hoover thermostat, parinello-rahman pressure coupling, and pme. Runnin the simulation in parallel is no problem (using 16 CPUs). However when I want to run an almost identical molecu

Re: [gmx-users] OPLS-AA topologies for ATP

Hi, I recently made up a topology for ADP. You can probably modify it to ATP easily. I used native OPLS atom types based on the DNA parameters (http://rnp-group.genebee.msu.su/3d/ff.htm ). The charges are copied from CHARMM27. Also, there is one dihedral angle missing, again, copied from CHA

[gmx-users] PRODRG crash

Dear Justin, Actually, I used -d option because you said the atoms in the box must be half a bond length from the edges of box...I thought maybe this can be done by -d... With PRODRG I am unable to produce coordinate file a chain with less than three C atoms. I sketched the molecules: C-C ethane

Re: [gmx-users] PRODRG crash

Moeed wrote: Dear Justin, Actually, I used -d option because you said the atoms in the box must be half a bond length from the edges of box...I thought maybe this can be done by -d... My point was that you should not be using a combination of -box, -d, and -angles simultaneously. Use e

[gmx-users] Charmm without CMAP

Hi, I am using gromacs from the git repository which I downloaded 2 days back. Charmm has been implemented in this version. Is it possible to use the Charmm ff without CMAP with it? Regards Pooja -- Quaerendo Invenietis-Seek and you shall discover. -- gmx-users mailing listgmx-users@gromac

[gmx-users] standard state correction of delta G from a PMF

Dear Elio: First, you need to convert your PMF to a free energy difference between states. That means defining a boundary between, for example, bound and unbound states. The integrate your PMF over the bound and unbound states to get two dG values, and their difference is your free energy

Re: [gmx-users] Charmm without CMAP

Hi! You can choose cmap/no cmap when you run pdb2gmx. /Per Skickat från min iPhone 22 jun 2010 kl. 19:24 skrev Sai Pooja : > Hi, > > I am using gromacs from the git repository which I downloaded 2 days back. > Charmm has been implemented in this version. Is it possible to use the Charmm >

[gmx-users] grompp fatal error Unknown bond_atomtype

Hi Users, I am experiencing the following fatal error when I try using the grompp command. grompp -f mdout.mdp -r conf.gro -p topol.top . . . --- Program grompp, VERSION 4.0.99-dev-20100409-004 Source code file: toppush.c, line: 631 Fatal

Re: [gmx-users] Charmm without CMAP

Thanks! On Tue, Jun 22, 2010 at 2:07 PM, Per Larsson wrote: > Hi! > > You can choose cmap/no cmap when you run pdb2gmx. > > /Per > > Skickat från min iPhone > > 22 jun 2010 kl. 19:24 skrev Sai Pooja : > > > Hi, > > > > I am using gromacs from the git repository which I downloaded 2 days > back.

[gmx-users] output of the -hist option of the g_wham command

Hi all, I am trying to perform umbrella sampling along with the WHAM to get the PMF. I go over the "umbrella sampling" tutorial prepared by Justin. Everything seems OK to me except one point. I could not understand the output given by the hist option of the g_wham command. There, what does "histo

[gmx-users] building up a long polymer chain

Hello Justin, I created structure file for a 4-carbon repeating unit as follows: HETATM1 CAA DRG 1 14.260 -4.270 0.000 1.00 20.00 C HETATM2 1HAA DRG 1 14.175 -3.426 0.530 1.00 20.00 H HETATM3 2HAA DRG 1 15.050 -4.790 0.326

Re: [gmx-users] building up a long polymer chain

Moeed wrote: Hello Justin, I created structure file for a 4-carbon repeating unit as follows: HETATM1 CAA DRG 1 14.260 -4.270 0.000 1.00 20.00 C HETATM2 1HAA DRG 1 14.175 -3.426 0.530 1.00 20.00 H HETATM3 2HAA DRG 1 15.0

[gmx-users] free energy landscape question

Hi, I am trying to use g_sham to obtain free energy landscape from a simulation. I can obtain the .xpm files but I want to know if there is any way of obtaining the actual histogram (in a form of a ASCII matrix vith numerical values) to use it in some other plotting program to draw contour lines p

[gmx-users] grompp fatal error Unknown bond_atomtype

There's lots of information in the gromacs manual to show that the .atp file is not the only file that you must modify. My most important suggestion to you is that you should read the entire manual, possibly twice, before attempting to build new molecules. Gromacs manual, page 96: 5.3.1

[gmx-users] Re: chain ids (2)

Dear All, I am re-posting with some replies to my first message. > the cell demensions for .gro files are at the bottomn, you know, you right. There at the top for .pdb file, and it is just a unit cell, and not very trivial to center graphically. And when you answere somones question like