Re: [gmx-users] Help needed on using general amber force field (GAFF) in Gromacs

You might not use pdb2gmx for such task. Once you have generated topology in AMBER format with Antechamber in GAFF, you will need to use some tools like ambconv.pl or ambconv (one is Perl script and one is a C++ programme, check GROMACS' website) to convert those files into GROMACS format. T

[gmx-users] Help needed on using general amber force field (GAFF) in Gromacs

Hi all, I am using GAFF force field for Gromacs package to simulate MD of surfactant molecule. I know we can generate .top file using some simple command like pdb2gmx if we use gromos force field. I am just wondering whether I can do the similar thing when using GAFF force field. If you have any e

[gmx-users] how to run a gases diffusiion simulation

  hi to all i am currently using GROMACS to run a simulation of gases diffusion that includes hydrogen and oxygen gas . I am stuck at the part in which I have to replace water with oxygen gas using genbox command. I could no fond any .gro file for oxygen or hydrogen gas How I can include the g

Re: [gmx-users] converged to Epot

Liu Shiyong wrote: Hi, Now, I do minimization. It's converged to Fmax < 100. How can I change it into Epot ? For example, Epot(n)-Epot(n-1) / Epot(n-1) < 5% n is the step. If you read the log file, you will see information that you can use in this way. Mark ___

[gmx-users] converged to Epot

Hi, Now, I do minimization. It's converged to Fmax < 100. How can I change it into Epot ? For example, Epot(n)-Epot(n-1) / Epot(n-1) < 5% n is the step. Step= 1891, Dmax= 1.2e-03 nm, Epot= -4.08327e+04 Fmax= 1.31834e+03, atom= 6946 Step= 1892, Dmax= 1.5e-03 nm, Epot= -4.08334e+04 Fmax= 9.46

Re: [gmx-users] How to change the default value for pbc ?

Thanks. It's exactly what you said. ePBC = no On Thu, Mar 13, 2008 at 6:44 PM, Alan Dodd <[EMAIL PROTECTED]> wrote: > Editing mdout.mdp will not affect the parameters in your .tpr, and > therefore your simulation, I'm fairly sure. It's just a report of what > you've spe

Re: [gmx-users] How to change the default value for pbc ?

Editing mdout.mdp will not affect the parameters in your .tpr, and therefore your simulation, I'm fairly sure. It's just a report of what you've specified, with all the defaults. Add the pbc=whatever line into your INPUT mdp to fix this. - Original Message From: Liu Shiyong <[EMAIL PR

[gmx-users] How to change the default value for pbc ?

Hi, I generated mdout.mdp by grompp -f em.mdp -c ${file}_box.gro -p ${file}.top -o ${file}.input.tpr . The pbc in mdout.mdp is like: ; Periodic boundary conditions: xyz (default), no (vacuum) ; or full (infinite systems only) pbc = xyz It seems that grompp doesnot give

[gmx-users] Umbrella sampling using 3-dimensions

Hello everyone, I would like to clarify exactly what is restrained in a simulation when doing umbrella sampling, using "pulldim = Y Y Y" in the .ppa input file. Consider you have the following in the .ppa file: verbose = no runtype = umbrella ngroups

Re: [gmx-users] Acetyl capping and Range checking error

Quoting Mauro Puppett <[EMAIL PROTECTED]>: > > Hi all, > I'm trying to run the simulation of a proline with an acetyl group on the N > terminus and an NH2 on the C. > I've already chenged the name of the residues on the pdb file, this way: > HETATM1 NPRO 1 -0.650 -0.337 0.028 >

[gmx-users] Acetyl capping and Range checking error

Hi all, I'm trying to run the simulation of a proline with an acetyl group on the N terminus and an NH2 on the C. I've already chenged the name of the residues on the pdb file, this way: HETATM1 NPRO 1 -0.650 -0.337 0.028 HETATM2 CA PRO 1 0.700 -0.304 -0.532

Re: [gmx-users] selecting residues which are within cutoff distances

I think g_dist with the option -dist will do what you want Tom --On Thursday, March 13, 2008 16:20:15 +0100 maria goranovic <[EMAIL PROTECTED]> wrote: Hello Folks, I have a protein trajectory to analyze. The goal is to find all residues within a 6 Angstrom radius of another residue, and lis

[gmx-users] selecting residues which are within cutoff distances

Hello Folks, I have a protein trajectory to analyze. The goal is to find all residues within a 6 Angstrom radius of another residue, and list their names (for example) over a trajectory. How can one do this ? I tried using g_mdmat. However, the eps generated by using xps2pm does not really convey

[gmx-users] Re: gmx-users Digest, Vol 47, Issue 41

t > happening like this? > Pls help me. > Thanks in advance. > -- next part -- > An HTML attachment was scrubbed... > URL: > http://www.gromacs.org/pipermail/gmx-users/attachments/20080313/9258929c/attachment-0001.html > > --

Re: [gmx-users] downloading problem

Siavoush Dastmalchi wrote: Hi there, This may not be relevant to this list but I am hopping to get an answer. The problem is that I can't download the source code for Grommacs from the download site and it seems that the link to web interface to the ftp server is not working as well. I tried

[gmx-users] downloading problem

Hi there, This may not be relevant to this list but I am hopping to get an answer. The problem is that I can't download the source code for Grommacs from the download site and it seems that the link to web interface to the ftp server is not working as well. I tried to use an ftp program to con

Re: [gmx-users] problem with mpi configuration.

Dr. Niharendu Choudhury wrote: Dear Pohl, I think your prefix directory /usr/local/gromacs332 is not accesible for writting. Try to creat new directories with other names and use those in prefix. First, they need to fix their typo in their configure command line, as mentioned by another post

Re: [gmx-users] problem with mpi configuration.

Dear Pohl, I think your prefix directory /usr/local/gromacs332 is not accesible for writting. Try to creat new directories with other names and use those in prefix. Have you setenv for the include and lib of the fftw files? (For instance, assume we have installed FFTW with --prefix=/home/joe/ff

Re: [gmx-users] Problem about *pdbgmx

sudheer babu wrote: Hi gmx-users, I want to protonate only HIS residues in my protein , so I gave command like this *pdb2gmx -f protein.pdb -HIS then it asked which number of HIS to protonate, I gave numbers of HIS residues which I want protonate , it ran fine without error, but when I open

[gmx-users] Problem about *pdbgmx

Hi gmx-users, I want to protonate only HIS residues in my protein , so I gave command like this *pdb2gmx -f protein.pdb -HIS then it asked which number of HIS to protonate, I gave numbers of HIS residues which I want protonate , it ran fine without error, but when I open conf.gro file, along wit

Re: [gmx-users] problem with mpi configuration.

> -Ursprüngliche Nachricht- > Von: Discussion list for GROMACS users > Gesendet: 12.03.08 20:06:55 > An: Discussion list for GROMACS users > Betreff: Re: [gmx-users] problem with mpi configuration. > Thank you very much for help me. > I have try to install gromacs 3.3.3 on rhel 4.0.