RE: [gmx-users] g_polystat

> Date: Sat, 4 Sep 2010 17:50:46 -0400 > From: jalem...@vt.edu > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] g_polystat > > > > Moeed wrote: > > Hello Justin, > > > > I have read help of the command I am using several times. My > > understanding is that g_polystat calculates Rg of

Re: [gmx-users] Protein stability using MARTINI

- Original Message - From: Itamar Kass Date: Monday, September 6, 2010 14:06 Subject: [gmx-users] Protein stability using MARTINI To: Discussion list for GROMACS users > HI all, > > I am simulating a protein in water using the MARTINI (CG) force > field. My protein composed of few a

[gmx-users] the broken of the molecules

 Hello, I do the energy minimization of the butylene box , but some butylene molecules are broken after that. The butylene itp file is produced by PRODRG, as follows:   [ moleculetype ] ; Name nrexcl BUT  3 [ atoms ] ;   nr  type  resnr resid  atom  cgnr   charge mass 1   C

Re: [gmx-users] the broken of the molecules

Hi, If I guess you correctly, you probably mean that when you look on your results (using VMD) it seems like it broken. If this is the case, you are OK, it might seems so but it is not, if you indeed used PBC. Best, Itamar On 6/09/2010 6:25 PM, kecy...@sina.com wrote: Hello, I do the ener

[gmx-users] grompp_d and mdrun_d issues with GBSA and normal mode analysis

Dear GROMACS users, I am encountering a couple of issues when trying to perform normal mode analysis in an implicit solvent (GBSA) setting. I am using version 4.5.1 with double precision; unfortunately I do not have the single precision version installed for comparison. The starting point

Re: [gmx-users] Protein stability using MARTINI

Thanks Mark for the replay, I used VDW presentation to over come it. Best, Itamar On 6/09/2010 6:33 PM, Mark Abraham wrote: - Original Message - From: Itamar Kass Date: Monday, September 6, 2010 14:06 Subject: [gmx-users] Protein stability using MARTINI To: Discussion list for GRO

Re: [gmx-users] Protein stability using MARTINI

Dear Itamar, If your problem is not a bond length definition in VMD (which you can overcome by using "dynamic bonds", although it is not perfect) you may have a problem in your topology. The way you describe your problem (groups of bids moving freely) suggests that you do have a topology proble

Re: [gmx-users] the broken of the molecules

Hi, If you are using PBC, mdrun will sometimes write sets of coordinates such that molecules appear "broken" across periodic boundaries. See http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions for solution approaches. Linear species can sometimes have other problems,

Re: [gmx-users] Protein stability using MARTINI

Hey, It might also be related to the PBC, with gromacs not writing whole molecules anymore. Maybe a link to a picture would be good, showing protein beads spheres, together with the (triclinic) unit cell. Cheers, Tsjerk On Mon, Sep 6, 2010 at 12:05 PM, XAvier Periole wrote: > > Dear Itamar, >

[gmx-users] PMF

Hi All I have generated a potential of mean force curve for two cage molecules. The profile of the curve is very good apart from the fact that the repulsive part of the curve doesn't go above zero. My attractive tail therefore appears higher than the repulsive part. The histograms are very well be

Re: [gmx-users] grompp_d and mdrun_d issues with GBSA and normal mode analysis

Hi! This should work. I checked the code but did not find anything obvious. Could you please file a bugzilla and I'll have a look as soon as possible. Thanks! /Per 6 sep 2010 kl. 11.38 skrev Ehud Schreiber: > Dear GROMACS users, > > I am encountering a couple of issues when trying to perform

Re: [gmx-users] g_covar & g_anaeig problems

Hey everyone, searching the list for the answer to a g_covar problem I've found this post of Arne who describes the very same problem that I encounter. I'm observing this problem on a linux cluster with 32GB memory on each node. The g_covar_d application was compiled in double precision with

[gmx-users] Problems with CMake and shared libraries

Hi All, I've discovered a new problem when using CMake. To recap, the system in question is a PowerPC cluster running Yellowdog Linux with OpenMPI-1.4.2 and gcc-4.2.2, linking against FFTW 3.0.1. I gave the following commands to build mdrun with CMake: cmake ../gromacs-4.5.1 -DFFTW3F_LIBRARIE

[gmx-users] ffamber03 H0 atomtype in 4.5.1

Hello Gromacs users, I have recently set up some simulations of a peptide using the amber03 force field in 4.5.1 and implicit solvent. When I run it through grompp, it gives me the following: --- Program grompp-4.5.1, VERSION 4.5.1 Source co

Re: [gmx-users] ffamber03 H0 atomtype in 4.5.1

Hi! This seems to be an unfortunate mistake. It should not be commented out. Thank you for reporting this, I will fix it for the next release. Cheers /Per 6 sep 2010 kl. 17.08 skrev William Joseph Allen: > Hello Gromacs users, > > I have recently set up some simulations of a peptide using the

Re: [gmx-users] Problems with CMake and shared libraries

Hi, Indeed, the custom cmake target "install-mdrun" was designed to only install the mdrun binary and it does not install the libraries this is linked against when BUILD_SHARED_LIBS=ON. I'm not completely sure that this is actually a bug, but to me it smells like one. I'll file a bug report and w

[gmx-users] pdb2gmx -chainsep vs -merge

Dear Gromacs Users, Has anybody merged all chains in a PDB file using -chainsep. because -chainsep does not seem to work. http://www.mail-archive.com/gmx-users@gromacs.org/msg33192.html Is there a alternate way of doing it ?, One way I could think of is to add the atoms numbers in the  topologi

Re: [gmx-users] pdb2gmx -chainsep vs -merge

nahren manuel wrote: Dear Gromacs Users, Has anybody merged all chains in a PDB file using -chainsep. because -chainsep does not seem to work. http://www.mail-archive.com/gmx-users@gromacs.org/msg33192.html Is there a alternate way of doing it ?, One way I could think of is to add the atoms

[gmx-users] about rdf

Hello, 1- In the manual I see rdf plot for Oxygen-Oxygen of SPC-water. I think this shows the average O-O density between all water molecules. I read a post saying that rdf is calculating C_C distances for each C on chain 1 for instance and all other C on the chain and other chains.. http://lists

Re: [gmx-users] about rdf

Moeed wrote: Hello, 1- In the manual I see rdf plot for Oxygen-Oxygen of SPC-water. I think this shows the average O-O density between all water molecules. I read a post saying that rdf is calculating C_C distances for each C on chain 1 for instance and all other C on the chain and other c

Re: [gmx-users] pdb2gmx -chainsep vs -merge

- Original Message - From: nahren manuel Date: Tuesday, September 7, 2010 7:16 Subject: [gmx-users] pdb2gmx -chainsep vs -merge To: gromacs gromacs --- | > Dear Gromacs Users, > Has anybody merged all chains in a PDB file using -c

Re: [gmx-users] g_covar & g_anaeig problems

- Original Message - From: Sebastian Breuers Date: Tuesday, September 7, 2010 0:42 Subject: Re: [gmx-users] g_covar & g_anaeig problems To: gmx-users@gromacs.org > Hey everyone, > > searching the list for the answer to a g_covar problem I've > found this post of Arne who describes the