Re: [gmx-users] Converting Gromacs output files to dl_poly output files.

Dear Naimah, Thanks a lot for the files that you send. I know the DL_POLY code create only site-site radial distribution functions (g(r)) as an OUTPUT file named RDFDAT. Indeed, DL_POLY can not create the Spatial Distribution Functions (SDFs) directly and I am not familiar with any proposed progra

[gmx-users] problem with the size of freeze groups

Dear Gromacs Users, I would like to compare the diffusion coefficient of water in different confined spheres with the bulk solvent, I have taken a solvent box of size 7nm, and I have created a sphere with radius 25 Å as lowest and 35 Å as highest spheres. I have not used the pressure coupling for

Re: Fwd: Re: [gmx-users] Re: Inconsisten shift Error

On 25/02/2010 6:07 AM, tekle...@ualberta.ca wrote: Hi Mark, Can you please help or comment on this problem ... I spent lots of time on running this simulation but failed to pass this stage until now... No. As you should know from reading the mailing list during all this time you've been

Re: [gmx-users] value of an angle

Carla Jamous wrote: Hi everyone, please I'm trying to find a way to calculate the value of an angle during the time of my simulation. g_angle calculates a distribution or an average. If you're only interested in a single angle, then g_angle -ov (with a suitable index group) does what you w

[gmx-users] value of an angle

Hi everyone, please I'm trying to find a way to calculate the value of an angle during the time of my simulation. g_angle calculates a distribution or an average. Thanks, Carla -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the

Re: [gmx-users] Re: Inconsisten shift Error

tekle...@ualberta.ca wrote: Hi Justine, Here is the procedure I followed…. I developed my PDB structure (non-protein means it is a polymer called PAP) using Material studio…. Get the PDB file and process it using the PRODRG…. I got both the GRO and TOP files………. However, PRODRG gave me a

Re: [gmx-users] problem in g_rdf using only x and y

Rebeca García Fandiño wrote: Thank you very much. One question, how should I use it? Should I compile Gromacs again? Yes. Changes to the source code require re-compilation and installation. I'll add my thanks to Berk as well :) -Justin Cheers, Rebeca. ---

RE: [gmx-users] problem in g_rdf using only x and y

Thank you very much. One question, how should I use it? Should I compile Gromacs again? Cheers, Rebeca. From: g...@hotmail.com To: jalem...@vt.edu; gmx-users@gromacs.org Subject: RE: [gmx-users] problem in g_rdf using only x and y Date: Wed, 24 Feb 2010 15:29:49 +0100 CC: Hi, I realize

RE: [gmx-users] problem in g_rdf using only x and y

Hi, I realize now that I committed a fix for this bug 3 days after the release of 4.0.7 (and not 3 days before the release as I initially thought). If you need it right now, I put the fixed source at: http://hess.cbr.su.se/~hess/gmx_rdf.c Berk > Date: Wed, 24 Feb 2010 06:52:57 -0500 > From: ja

RE: [gmx-users] density

> Date: Wed, 24 Feb 2010 14:46:17 +0100 > From: sp...@xray.bmc.uu.se > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] density > > On 2/24/10 2:00 PM, Sander Pronk wrote: > > You got pretty close to what the density of SPC water is at 298K > > > > According to "Temperature dependence of TI

Re: [gmx-users] density

On 2/24/10 2:00 PM, Sander Pronk wrote: You got pretty close to what the density of SPC water is at 298K According to "Temperature dependence of TIP3P, SPC, and TIP4P water from NPT Monte Carlo simulations: Seeking temperatures of maximum density", William L. Jorgensen, Corky Jenson, J. Comp. Ch

RE: [gmx-users] Converting Gromacs output files to dl_poly output files.

Dear naimah, I have certainly inverse problem. I simulated several imidazolium-based ILs by DL_POLY code using of all- atom Canongia Lopes force field parameters (JPC B 2004); but now I like more study these liquids by GROMACS code. I think that you should firstly convert GROMACS input files (*.gr

Re: [gmx-users] density

You got pretty close to what the density of SPC water is at 298K According to "Temperature dependence of TIP3P, SPC, and TIP4P water from NPT Monte Carlo simulations: Seeking temperatures of maximum density", William L. Jorgensen, Corky Jenson, J. Comp. Chem, Volume 19 Issue 10, Pages 1179 - 118

Re: [gmx-users] density

On 2/24/10 1:23 PM, Sunil Thapa wrote: Respectable Experts Grettings I am studying diffusion of an oxygen molecule in 255 molecule of SPC water. I need to determine diffusion coefficient at temperature 298 K and 1 atm pressure. In order to do that using editconf I scaled the density of the system

[gmx-users] density

Respectable Experts Grettings I am studying diffusion of an oxygen molecule in 255 molecule of SPC water. I need to determine diffusion coefficient at temperature 298 K and 1 atm pressure. In order to do that using editconf I scaled the density of the system including oxygen to 1g/l. I checked t

Re: [gmx-users] problem in g_rdf using only x and y

Berk Hess wrote: Well, I fixed a bug with g_rdf -xy before the 4.0.7 release. But apparently this fix does not work under all conditions. Could one of you file a bugzilla and attach a tpr file and a trajectory, preferably with only one or very few frames and write the exact command line? Fil

RE: [gmx-users] problem in g_rdf using only x and y

Well, I fixed a bug with g_rdf -xy before the 4.0.7 release. But apparently this fix does not work under all conditions. Could one of you file a bugzilla and attach a tpr file and a trajectory, preferably with only one or very few frames and write the exact command line? Thanks, Berk > Date: Tu