RE: [gmx-users] Hard Spheres

Subject: Re: [gmx-users] Hard Spheres From: sascha.hem...@bci.tu-dortmund.de To: gmx-users@gromacs.org Date: Thu, 9 Dec 2010 08:56:54 +0100 On Wed, Dec 8, 2010 at 4:01 AM, Sascha Hempel sascha.hem...@bci.tu-dortmund.de wrote: Hi all! I am trying to add

[gmx-users] water-air interface surface tension

Hi, experts, I'd like to calculate the surface tension at water-air interface using Gromacs. which ensemble should i choose? when i run simulation, .mdp how can i select p-coupling? whether should i use p-coupling? I can creat a air-water-air structure (.gro) Thanks?-- gmx-users mailing

Re: [gmx-users] water-air interface surface tension

On 2010-12-09 09.20, gromacs wrote: Hi, experts, I'd like to calculate the surface tension at water-air interface using Gromacs. which ensemble should i choose? when i run simulation, .mdp how can i select p-coupling? whether should i use p-coupling? what do you think will happen when you use P

RE: [gmx-users] Hard Spheres

On Thu, 2010-12-09 at 09:11 +0100, Berk Hess wrote: Subject: Re: [gmx-users] Hard Spheres From: sascha.hem...@bci.tu-dortmund.de To: gmx-users@gromacs.org Date: Thu, 9 Dec 2010 08:56:54 +0100 On Wed, Dec 8, 2010 at 4:01 AM, Sascha Hempel sascha.hem...@bci.tu-dortmund.de wrote:

[gmx-users] Can the g_order calculate order parameters for two polymer backbone atoms?

Dear gmxers, I am planning to analyze order parameter using g_order, but some problems always puzzle me. For convenience, I describe the first problem as follows: Assume that there are two polymer chains H-[CH2-CH(OH)]n-H, now I want to calculate the order parameter of two carbon atoms in

Re: [gmx-users] water-air interface surface tension

Hi David Can you tell me which journal, volume and page number. I am not able to acess the link you have given. any help is highly appreciated Regards Vinoth 2010/12/9 David van der Spoel sp...@xray.bmc.uu.se On 2010-12-09 09.20, gromacs wrote: Hi, experts, I'd like to calculate the

[gmx-users] Pull simulation odditites when viewed in VMD

Hey, I've been performing a pull simulation of a protein, all seems to work fine however after I convert the .xtc file into seperate .gro files and load those into VMD to visualise the simulation something weird happens. Every 50 frames or so a random bond within the backbone of the protein

Re: [gmx-users] Pull simulation odditites when viewed in VMD

Natalie Stephenson wrote: Hey, I've been performing a pull simulation of a protein, all seems to work fine however after I convert the .xtc file into seperate .gro files and load those into VMD to visualise the simulation something weird happens. Every 50 frames or so a random bond within

Re: [gmx-users] Hard Spheres

On 09/12/10 09:51, Sascha Hempel wrote: Thanks for your advice. I looked this up in the manual and experimented a little with the functions. I can not just set C6 to 0 beacause then i will keep a repulsing potential at long distances which will skrew with my system. I could use a shift or

[gmx-users] crashed run

Dear friends Thanks for help I did what you said. but now I have another question. why when I compute RMSD, there is a turbulence in the digits between two MD runs (MD1 MD2)? Along 10nS RMSD values increase but after that in continued MD RMSD values start with lower digits. So the obtained RMSD

Re: [gmx-users] crashed run

shiva birgani wrote: Dear friends Thanks for help I did what you said. but now I have another question. why when I compute RMSD, there is a turbulence in the digits between two MD runs (MD1 MD2)? Along 10nS RMSD values increase but after that in continued MD RMSD values start with lower

RE: [gmx-users] Pull simulation odditites when viewed in VMD

Thanks loads for that!! I hadn't realised it was that simple! Natalie xxx From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin A. Lemkul [jalem...@vt.edu] Sent: 09 December 2010 12:05 To: Discussion list for GROMACS

[gmx-users] g_wham

Hello I am trying run g_wham for umbrella sampling. Before going for sampling I want to plot PMF. I have one .tpr file and one one pullf.xvg. How can I use them to run PF Nilesh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please

Re: [gmx-users] g_wham

Nilesh Dhumal wrote: Hello I am trying run g_wham for umbrella sampling. Before going for sampling I want to plot PMF. I have one .tpr file and one one pullf.xvg. How can I use them to run PF You can't. Umbrella sampling implies that you've done simulations in multiple sampling windows

[gmx-users] -sel option for g_hbond

Dear Gromacs users, Does some one know if -sel option for g_hbond command is working in gromacs beta 4.5. Because when I try to run fir individual Hbonds privided in second index file gromacs can not recognize -sel command. Yours sincerely, Olga -- gmx-users mailing list

[gmx-users] How to force gromacs to fix all bad bonds and angles in a homology model?

Hi, all, I am looking for a way in gromacs or manually to make all the angles, etc. ideal. Perhaps, there is a way to energy minimize a specific subset of residues or a single residue. Your advice would be greatly appreciated. Sincerely, Art Dr. Arthur Roberts, Ph.D. University of

[gmx-users] Re: gmx-users Digest, Vol 80, Issue 64

Dear Justin So thanks for your help. you are right. I had put a wrong .rtp file With regards Shiva -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before

Re: [gmx-users] -sel option for g_hbond

Olga Ivchenko wrote: Dear Gromacs users, Does some one know if -sel option for g_hbond command is working in gromacs beta 4.5. Because when I try to run fir individual Hbonds privided in second index file gromacs can not recognize -sel command. I don't think the -sel option has worked

Re: [gmx-users] How to force gromacs to fix all bad bonds and angles in a homology model?

Arthur Roberts wrote: Hi, all, I am looking for a way in gromacs or manually to make all the angles, etc. ideal. Perhaps, there is a way to energy minimize a specific subset of residues or a single residue. Your advice would be greatly appreciated. Couldn't you just specify very

[gmx-users] How to obtain the semi-axis lengths from inertia tensor for an aggregate

Dear all, I would to obtain the semi-axis lengths of a simulated micelle (in Ang) with gromacs. So I have used the g_principal tool (correct ?). My input command was g_principal_mpi -f bDM-Self_Only_DDM_Center.xtc -s bDM_only.tpr -a1 bDM_Self_Axe1 -a2 bDM_Self_Axe2 -a3 bDM_Self_Axe3 -om

[gmx-users] g_anaeig

I am postin ths question second time so please solve this issue g_anaeig generated numbers of c-alpha or protein structures through -extr extreme.pdb. The bash shell show numbers of eigenvector structures starting from first to last frames are as follows eigenvector Minimum

Re: [gmx-users] g_anaeig

pawan raghav wrote: I am postin ths question second time so please solve this issue g_anaeig generated numbers of c-alpha or protein structures through -extr extreme.pdb. The bash shell show numbers of eigenvector structures starting from first to last frames are as follows eigenvector

[gmx-users] CMAP error

Dear all, I am setting up a system with GROMACS 4.5.3 and the CHARMM force field. In the protein, I have a neutral lysine, for which CHARMM force filed has a specific residue type (LSN). When I wrote LSN as residue name in the initial pdb file, the topology file was perfectly created by pdb2gmx.

Re: [gmx-users] CMAP error

Jon Mujika wrote: Dear all, I am setting up a system with GROMACS 4.5.3 and the CHARMM force field. In the protein, I have a neutral lysine, for which CHARMM force filed has a specific residue type (LSN). When I wrote LSN as residue name in the initial pdb file, the topology file was

Re: [gmx-users] CMAP error

This may not be related but it was not straight forward to do DPPC membrane simulation using CHARMM FF in gromacs. The DPPC molecule was not defined at all in the FF files. The DPPC is defined in terms of two more residues in CHARMM. amit On Thu, Dec 9, 2010 at 11:21 AM, Justin A. Lemkul

Re: [gmx-users] CMAP error

This is a completely separate issue where the CHARMM force field files from which the GROMACS CHARMM27 rtp entries were created do not have a DPPC entry, rather DPPC in CHARMM is created from using two residues (PALM and PCGL) and two patches (EST1 and EST2). It should have been easy enough to

[gmx-users] gb_saltconc in implicit water simulations

Hello everyone, I am trying to use implicit solvent with a CG DNA model. The model, however, uses explicit charges, which means that the DNA carries an overall negative charge. When using implicit solvent with a charged system in other codes (e.g. Amber), the electrolyte is taken care of

[gmx-users] What might be the process if we wanted to sim a peptide + a peptide?

Dear Gromacs Users, Can we perform gromacs analysis on any two molecules like peptide+ peptide or DNA+ RNA? and what might be the setup and process if we wanted to sim a peptide + a peptide with a small molecule causing a PTM event. If we can do so then do we have any options to select two

Re: [gmx-users] What might be the process if we wanted to sim a peptide + a peptide?

swati shah wrote: Dear Gromacs Users, Can we perform gromacs analysis on any two molecules like peptide+ peptide or DNA+ RNA? and what might be the setup and process if we wanted to sim a peptide + a peptide with a small molecule causing a PTM event. If we can do so then do we have any

[gmx-users] Seeking advice on how to build Gromacs on Teragrid resources

Hello gmx users! I realize this may be a touch off topic, but I am hoping that someone out there can offer some advice on how to build Gromacs for parallel use on a Teragrid site. Our group is currently using Abe on Teragrid, and unfortunately the latest version of Gromacs compiled for public use

Re: [gmx-users] Seeking advice on how to build Gromacs on Teragrid resources

On 10/12/2010 9:14 AM, J. Nathan Scott wrote: Hello gmx users! I realize this may be a touch off topic, but I am hoping that someone out there can offer some advice on how to build Gromacs for parallel use on a Teragrid site. Our group is currently using Abe on Teragrid, and unfortunately the

Re: [gmx-users] How to force gromacs to fix all bad bonds and angles in a homology model?

This is a bit off-topic but if you want to improve dihedral angles, bond angles and distances, rotamers along with steric clashes, IMO PyRosetta is more efficient than GROMACS. I use ClassicRelax protocol with the 'standard' score function in conjunction with the 'score12' patch ('score12' patch

[gmx-users] Which FF could be used for protein-RNA MD simulation in GROMACS?

Hi, I just tried G53a6 for protein-RNA simulation. But fatal error shows up. Opening library file /usr/share/gromacs/top//FF.dat Select the Force Field: 0: GROMOS96 43a1 force field 1: GROMOS96 43a2 force field (improved alkane dihedrals) 2: GROMOS96 45a3 force field (Schuler JCC 2001 22

Re: [gmx-users] Which FF could be used for protein-RNA MD simulation in GROMACS?

Liu Shiyong wrote: Hi, I just tried G53a6 for protein-RNA simulation. But fatal error shows up. That's a useless description of the problem. Exact input and output would be necessary to diagnose the problem. Regardless, the choice of Gromos is a particularly bad one for nucleic acid

[gmx-users] Re: Which FF could be used for protein-RNA MD simulation in GROMACS?

Hey, Shiyong - I believe your problem is related to X2TOP usage rather than to a proper force field choice. I'd suggest to start with looking into N2T files for the below entries. Cheers. -- Dr. Vitaly V. Chaban Rochester, U.S.A.  I just tried G53a6 for protein-RNA simulation. But fatal

Re: [gmx-users] Re: Which FF could be used for protein-RNA MD simulation in GROMACS?

Vitaly Chaban wrote: Hey, Shiyong - I believe your problem is related to X2TOP usage rather than to a proper force field choice. I'd suggest to start with looking into N2T files for the below entries. The output posted is from pdb2gmx. It is also unlikely that x2top would be of any use

Re: [gmx-users] Which FF could be used for protein-RNA MD simulation in GROMACS?

Thanks. I will upgrade to Version 4.5 and use AMBER. I like G53a6, but it surprised me without RNA parameter. On Fri, Dec 10, 2010 at 11:57 AM, Justin A. Lemkul jalem...@vt.edu wrote: Liu Shiyong wrote: Hi,  I just tried G53a6 for protein-RNA simulation. But fatal error shows up.

[gmx-users] g_anaeig

Dear justin, Thanks for your useful suggestions but not the right way to post these things. Anyway Dear I have already read the link mentioned by you and know very well what does -extr do actually I want to extract some minimum energy structure for docking studies from 12500 ps to 15000 ps MD

Re: [gmx-users] Seeking advice on how to build Gromacs on Teragrid resources

What MVAPICH version are you using? Are you using a TPR file you know is running fine on some other machine? Does the 4.5.2 version they installed run correct? If so what is the configure line they used? Roland On Thu, Dec 9, 2010 at 5:14 PM, J. Nathan Scott scot...@chemistry.montana.edu