Re: [gmx-users] What if there are multi-definition of dihedrals?

Hi Wu Yanbin, Multiple definitions are combined. (Isn't this in the manual?) Tsjerk On 7/17/07, WU Yanbin <[EMAIL PROTECTED]> wrote: Hi, All, If there are multi-definitions of the same dihedral in topology file, how will gromacs treat it? Using the second one, or the addition of the two item

Re: [gmx-users] a) rlist vs rvdw/rcoulomb size confusion, and b) reduced units

So if you box size is 5 (as you say) and your cut-off is 1, then you should not get an error. So one of the two things is wrong. Maybe you made a pdb file with box 5? pdb is in Angstrom, while Gromacs uses nm, so there is a conversion factor of 0.1. Berk. That's what it was. Thanks a bunch. A f

Re: [gmx-users] a) rlist vs rvdw/rcoulomb size confusion, and b) reduced units

From: "Frankie Montenegro" <[EMAIL PROTECTED]> Reply-To: Discussion list for GROMACS users To: "Discussion list for GROMACS users" Subject: Re: [gmx-users] a) rlist vs rvdw/rcoulomb size confusion,and b) reduced units Date: Tue, 17 Jul 2007 03:41:46 -0400 So if you box size is 5 (as you

Re: [gmx-users] What if there are multi-definition of dihedrals?

Entries in [ bonds ], [ pairs ], [ angles ], [ dihedrals ] are additive. Repeat the entry for two or more times will effectively double or triple the energy. On 7/17/2007 3:02 PM, Tsjerk Wassenaar wrote: Hi Wu Yanbin, Multiple definitions are combined. (Isn't this in the manual?) Tsjerk On

Re: [gmx-users] a) rlist vs rvdw/rcoulomb size confusion, and b) reduced units

I think that what you want is inconsistent. If you want dispersion correction this means that in principle you do not want cut-off's. Berk, you are right: I don't want any cutoffs, I am trying to avoid them. But I thought the way Gromacs works is, if you don't choose one, you get assigned the d

[gmx-users] Error during grompp

Dear Gromacs users, During my last simulation of 2 ns a part of a protein moved out of the water box. When I've tried to proceed to the next 2 ns I've got the folowing message during grompp: Fatal error: number of coordinates in coordinate file (wt_md2_egf4.gro, 17346) does not match topo

Re: [gmx-users] which tool to use a measure a user-defined angle in a traj

Fair enough, but I'll just repeat that g_bundle does *exactly* what you want in your example - provide it with an index file with two groups with the COMs defining the ends of the axes (in your case, one C in one group and one O in the other) and the option -z, and it'll dump out a file of the a

Re: [gmx-users] Error during grompp

Yulia Einav wrote: Dear Gromacs users, During my last simulation of 2 ns a part of a protein moved out of the water box. When I've tried to proceed to the next 2 ns I've got the folowing message during grompp: Fatal error: number of coordinates in coordinate file (wt_md2_egf4.gro, 17346)

Re: [gmx-users] a) rlist vs rvdw/rcoulomb size confusion, and b) reduced units

From: "Frankie Montenegro" <[EMAIL PROTECTED]> Reply-To: Discussion list for GROMACS users To: "Discussion list for GROMACS users" Subject: Re: [gmx-users] a) rlist vs rvdw/rcoulomb size confusion,and b) reduced units Date: Tue, 17 Jul 2007 04:53:40 -0400 I think that what you want is i

Re: [gmx-users] Error during grompp

Running out of box is common and it actually doesn't because of PBC. You may just continue the simulation For this fatal error, you shall refer to how you have created the first tpr file: which top file you have used. On 7/17/2007 5:39 PM, Yulia Einav wrote: Dear Gromacs users, During my

[gmx-users] Re: gmx-users Digest, Vol 39, Issue 56

-- Message: 5 Date: Mon, 16 Jul 2007 16:39:29 +0200 From: "Jeroen van Bemmelen" < [EMAIL PROTECTED]> Subject: [gmx-users] Regarding polymer equillibration (pressure changes) To: gmx-users@gromacs.org Message-ID: < [EMAIL PROTECTED]> Content-Type: text/plain; c

Re: [gmx-users] Re: gmx-users Digest, Vol 39, Issue 56

ann rose wrote: -- Message: 5 Date: Mon, 16 Jul 2007 16:39:29 +0200 From: "Jeroen van Bemmelen" < [EMAIL PROTECTED] > Subject: [gmx-users] Regarding polymer equillibration (pressure changes) To: gmx-use

[gmx-users] free energy perturbations and B-parameter specifications

Dear Gromacsers, I have been doing free energy perturbations Gly->Ala in one strand of collagene. Now, the problem is that I have later closely reread the section 5.6.4 ("Free Energy Calculations") p. 105 in which it says: "Bonded interactions between atoms that are not perturbed d

Re: [gmx-users] free energy perturbations and B-parameter specifications

On Jul 17, 2007, at 4:45 PM, Soren Enemark wrote: Dear Gromacsers, I have been doing free energy perturbations Gly->Ala in one strand of collagene. Now, the problem is that I have later closely reread the section 5.6.4 ("Free Energy Calculations") p. 105 in which it says: "Bonded intera

[gmx-users] Constrains and TI

hello all, is it possible to constrain a distance (or several) between a ligand-receptor complex inorder to simulate free energy change of separating the ligand from the receptor? I intend to use TI and lamda to do free energy calculations. any help is appreicated. Belquis __

Re: [gmx-users] which tool to use a measure a user-defined angle in a traj

ok. I'll give it a shot too, should get the same answer , will be a good way to double check, Arneh Alan Dodd wrote: Fair enough, but I'll just repeat that g_bundle does *exactly* what you want in your example - provide it with an index file with two groups with the COMs defining the ends o

[gmx-users] ACE parameter error in ffG53a5/6?

Dear gmx-users I think that I have found an error in the files ffG53a(5 and 6).rtp related to ACE topology. Maybe it is a trivial error, but I’m sure someone of you will ponder it much better than me. I am constructing the topology for an N-acetylated 2-amino sugar (N- acetylgalactosamine) usin

[gmx-users] Parallel Use of gromacs - parallel run is 20 times SLOWER than single node run

I ran a parallel (mpi) compiled version of gromacs using the following command line: $ mpirun -np 5 mdrun_mpi -s topol.tpr -np 5 -v At the end of the file md0.log I found: M E G A - F L O P S A C C O U N T I N G Parallel run - timing based on wallclock. RF=Reaction-Field F

RE: [gmx-users] Error during grompp

> Furthemore the same part of the protein always move out of > the box in different simulations. > > Is there any way to prevent the moving? http://wiki.gromacs.org/index.php/Periodic_Boundary_Conditions Catch ya, Dr. Dallas Warren Lecturer Department of Pharmaceutical Biology and Pharmacolog

RE: [gmx-users] Re: gmx-users Digest, Vol 39, Issue 56

>3. How can i keep all my molecules inside the box during the simulation run? http://wiki.gromacs.org/index.php/Periodic_Boundary_Conditions Catch ya, Dr. Dallas Warren Lecturer Department of Pharmaceutical Biology and Pharmacology Victorian College of Pharmacy, Monash University 381 Royal Par

RE: [gmx-users] Parallel Use of gromacs - parallel run is 20 times SLOWER than single node run

Jim, What size system is it that you are simulating? Catch ya, Dr. Dallas Warren Lecturer Department of Pharmaceutical Biology and Pharmacology Victorian College of Pharmacy, Monash University 381 Royal Parade, Parkville VIC 3010 [EMAIL PROTECTED] +61 3 9903 9524 -

[gmx-users] phosphated residue???

Dear all There is a phosphate ser in my protein, so when pdb2gmx, the fatal error is "atom p is not found" How to deal with this problem? how to add the topology file of phosphate ion to residue database? Thank you! - 雅虎免费邮箱3.5G容量，20M附件！_

Re: [gmx-users] phosphated residue???

> Dear all There is a phosphate ser in my protein, so when pdb2gmx, the > fatal error is "atom p is not found" > >How to deal with this problem? how to add the topology file of > phosphate ion to residue database? You'll need the Gromos96 43a1p force field parameters. Check out use

[gmx-users] mdrun -rerun problems

Hi all, I am running simulations of carbon nanotubes and amino acids in water. I need to calculate the potential energies for the whole system as well as the interaction energy between the CNT and amino acid. What I am tried to do is to calculate the energy for the whole system first

[gmx-users] Runtime need of cpp.exe

Friends As I know cpp.exe is a GNU port for C Preprocessor for Windows and which is required to compile the Gromacs code. But I'm confused, Why it is required during runtime of Gromacs applications ? And I have the Win32 version of cpp.exe, will it work for x64 (=Win64) ? What is the Windows