Re: [gmx-users] Invalid command line argument: -np

Chih-Ying Lin wrote: Hi Since the -np flag is no longer necessary with grompp for the version 4.0, how to tell Gromacs the number of the nodes being compiled together ? It determines the maximum number available from your MPI environment and uses that. So your MPI configuration and/or your mpi

[gmx-users] Invalid command line argument: -np

Hi Since the -np flag is no longer necessary with grompp for the version 4.0, how to tell Gromacs the number of the nodes being compiled together ? Thank you Lin Chih-Ying Lin wrote: > > > Hi > I typed the command => > > grompp_mpi -np 16 -v -f md.mdp -c 6LYZ-MD5500.gro -p 6LYZ.top -o > 6L

Re: [gmx-users] Buckingham Potential

Andrew Paluch wrote: To whom this may concern, I am performing simulations for a system that is modeled with a Buckingham potential and PME for the electrostatic interactions. I have developed my forcefield file such that non-bonded cross terms are listed in a table, and also 1-4 interaction

Re: [gmx-users] Control Atoms for Hydroxide ?

Marc Charendoff wrote: Sorry for bringing up the hydroxide ion question again, but are there any hints as to how to place a single hydrogen on the oxygen atom? Can I somehow assign control atoms outside the hydroxide anion as a means of reference for the required ffG43a1.hdb modification? Loo

[gmx-users] table problems

HI everyone, I want to make a test using tables potential, I choose full-atoms benzene molecules for example.firstly ,I transform the 12-6 LJ potential into table potential, but when mdrun step, I got a error message as follows: *

[gmx-users] Control Atoms for Hydroxide ?

Sorry for bringing up the hydroxide ion question again, but are there any hints as to how to place a single hydrogen on the oxygen atom? Can I somehow assign control atoms outside the hydroxide anion as a means of reference for the required ffG43a1.hdb modification? Looks like both methods to a

Re: [gmx-users] shuffle switch

Paymon Pirzadeh wrote: Hello, I have a quick question about "-shuffle" switch in grompp. Do we still need to apply this option in 4.0.5 when we use parallel versions or not. There is no such option in 4.0.5. What's more, domain decomposition speeds up the calculations more than shuffling e

[gmx-users] shuffle switch

Hello, I have a quick question about "-shuffle" switch in grompp. Do we still need to apply this option in 4.0.5 when we use parallel versions or not. regards, Payman ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/

Re: [gmx-users] Invalid command line argument: -np

Nav Rajput wrote: Hi I think you can try this grompp_mpi -f md.mdp -c 6LYZ-MD5500.gro -p 6LYZ.top -o 6LYZ-MD6000.tpr -np 16 This is wrong. As I said before (and has been stated many times across this list), as of version 4.0, the -np option has been eliminated from grompp. There is

Re: [gmx-users] Invalid command line argument: -np

Hi I think you can try this grompp_mpi -f md.mdp -c 6LYZ-MD5500.gro -p 6LYZ.top -o 6LYZ-MD6000.tpr -np 16 On Mon, Aug 17, 2009 at 4:29 PM, Chih-Ying Lin wrote: > > > Hi > I typed the command => > > grompp_mpi -np 16 -v -f md.mdp -c 6LYZ-MD5500.gro -p 6LYZ.top -o > 6LYZ-MD6000.tpr > > > It sho

Re: [gmx-users] Invalid command line argument: -np

Chih-Ying Lin wrote: Hi I typed the command => grompp_mpi -np 16 -v -f md.mdp -c 6LYZ-MD5500.gro -p 6LYZ.top -o 6LYZ-MD6000.tpr It showed => Invalid command line argument: -np The above command works with 3.3.3 version but does not work with 4.0.5 version. I was checking grompp_mpi

[gmx-users] Invalid command line argument: -np

Hi I typed the command => grompp_mpi -np 16 -v -f md.mdp -c 6LYZ-MD5500.gro -p 6LYZ.top -o 6LYZ-MD6000.tpr It showed => Invalid command line argument: -np The above command works with 3.3.3 version but does not work with 4.0.5 version. I was checking grompp_mpi -h and cannot know the proper

Re: [gmx-users] Hydroxide Attempt

Marc Charendoff wrote: Hello, I am attempting to see if I can process and run a hydroxide ion using the ffG43a1 force field. In doing this I have read through chapter 5 of the manual and have a couple of questions. I do realize that the chemistry and physics of this will need to be j

[gmx-users] Hydroxide Attempt

Hello,     I am attempting to see if I can process and run a hydroxide ion using  the ffG43a1 force field. In doing this  I have read through chapter 5 of the manual and have a couple of questions. I do realize that the chemistry and physics of this will need to be justified, but at this point

[gmx-users] No default Ryckaert-Bell. types error for N-terminus acetylated peptide, opls-aa force field

the archive *can* still be searched from the "old" site: http://oldwww.gromacs.org/swish-e/search/search2.php Thanks Justin, this is very valuable information. I guess that this is where a new search link on the new website should point for now. Chris. -- original message -- chris.ne...@u

[gmx-users] Thanks for instruction on using xdr library

Hello everybody: I just received an email from Jussi Lehtola. I include : extern "C" { #include } in my source code, and it works. Thanks all. Kun ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users

[gmx-users] Re: help needed for using xdr library

Hi, Actually the xdrfile_xtc.h file did include the xdrfile.h. And I also tried to include xdrfile_xtc.h directly in my source file. The link error is still there. I really don't know what's the problem because the make test command passed. On Mon, Aug 17, 2009 at 1:34 PM, Vitaly V. Chaban wrote

Re: [gmx-users] help needed for using xdr library

On Mon, 2009-08-17 at 20:46 +0300, Jussi Lehtola wrote: > you need to use > > extern C { > #include > } Whoops, that should read extern "C" { -- -- Jussi Lehtola, FM, Tohtorikoulutettava Fysiikan laitos, Helsingin Yliopisto jussi.leht...@hels

Re: [gmx-users] help needed for using xdr library

On Mon, 2009-08-17 at 09:41 -0400, Kun Huang wrote: > Hello everyone: > > Recently I am trying to use the xdr library downloaded from gromacs > org to read xtc files. However when I link my program with the library > there is an error. When I ran the make test, all the tests were > passed. Thus I

Re: [gmx-users] No default Ryckaert-Bell. types error for N-terminus acetylated peptide, opls-aa force field

chris.ne...@utoronto.ca wrote: The inability to search the archives is certainly leading to some redundancy. I use google now, it does a decent job of digging up stuff from the gmx mailing list archives -- Even the oldwww search link takes me to the new site inside of the iframe so that is no

[gmx-users] Re: help needed for using xdr library

Hi, 1. It seems you also need to include xdrfile.h. 2. Are the library files located in the same directory with your source files when you link? VItaly > > Recently I am trying to use the xdr library downloaded from gromacs org to > read xtc files. However when I link my program with the library

[gmx-users] No default Ryckaert-Bell. types error for N-terminus acetylated peptide, opls-aa force field

The inability to search the archives is certainly leading to some redundancy. I use google now, it does a decent job of digging up stuff from the gmx mailing list archives -- Even the oldwww search link takes me to the new site inside of the iframe so that is no use. I suggest that the sear

[gmx-users] Buckingham Potential

To whom this may concern, I am performing simulations for a system that is modeled with a Buckingham potential and PME for the electrostatic interactions. I have developed my forcefield file such that non-bonded cross terms are listed in a table, and also 1-4 interactions are listed in a

[gmx-users] No default Ryckaert-Bell. types error for N-terminus acetylated peptide, opls-aa force field

I am trying to solvate a peptide which has an acetylated N-terminus in the opls-aa force field. Running pdb2gmx (v. 4.0.2) gives me the following error: Error 1 No default Ryckaert-Bell types. The guilty atoms in the topology are 4 atoms at the N-terminus. This issue has been raised before as wel

[gmx-users] help needed for using xdr library

Hello everyone: Recently I am trying to use the xdr library downloaded from gromacs org to read xtc files. However when I link my program with the library there is an error. When I ran the make test, all the tests were passed. Thus I think that the library should work just I don't know how to link

Re: [Fwd: [gmx-users] preferred/best force fields]

iu...@interponta.com.br wrote: Hi, I see there are many interesting topics going on, maybe due to this I did not receive any answer/suggestion/comment to my question or maybe it is rather naive. Anyway, it would like to listen to the experts if there are no other suggestions to add to wha

[Fwd: [gmx-users] preferred/best force fields]

Hi, I see there are many interesting topics going on, maybe due to this I did not receive any answer/suggestion/comment to my question or maybe it is rather naive. Anyway, it would like to listen to the experts if there are no other suggestions to add to what I did below. Thanks,

Re: [gmx-users] Spacing

P.R.Anand Narayanan wrote: Dear gromacs users, I've been using gromacs to run a simulation of a protein with a cofactor and a ligand. i had a problem while running the simulation; the cofactor, ligand and the substrate molecule were spaced away from the protein in the solvent box., thereby

[gmx-users] Spacing

Dear gromacs users, I've been using gromacs to run a simulation of  a protein with a cofactor and a ligand. i had a problem while running the simulation; the cofactor, ligand and the substrate molecule were spaced away from the protein in the solvent box., thereby creating literally zero interac

RE: [gmx-users] topolbuild1_2_1.tgz decompressing problem

I had the similar problem but I untar it in two step to get around it: 1st gunzip *.tgz 2nd tar it in usual without z option > Date: Mon, 17 Aug 2009 08:25:15 +0200 > From: sp...@xray.bmc.uu.se > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] topolbuild1_2_1.tgz decompressing