Re: [gmx-users] Problems with GROMPP

It might be helpful to post to the list the exact commands you issued so far. It might be illustrative of the problem. -Justin Tried it with bash and tcsh. pdb2gmx: -f *.pdb -o *.gro -p -q *.pdb -n -i opls-forcefield (no.6) editconf: -f *.gro -o -bt cubic -d 0.1 -vol genbox: -cp *.gro

Re: [gmx-users] Problems with GROMPP

Jens Pohl wrote: It might be helpful to post to the list the exact commands you issued so far. It might be illustrative of the problem. -Justin Tried it with bash and tcsh. pdb2gmx: -f *.pdb -o *.gro -p -q *.pdb -n -i opls-forcefield (no.6) editconf: -f *.gro -o -bt cubic -d 0.1 -vol

Re: [gmx-users] Problems with GROMPP

I'd echo Justin's request for your *actual* commands. Computers are very literal, and we'd rather have your original commands than something that's clearly been filtered through your head. If the above reflects your actual use of wildcards on the command line, that sounds like a possible

[gmx-users] Go-model Hamiltonian

Greetings Gromax users! I am trying to do free energy calculations using a Go-model Hamiltonian simulation, and I was wondering if GROMACS has such capabilities. I was planning to use CHARMM but I found a problem at a server that builds the respective Go-model Hamiltonian from a pdb file

[gmx-users] image control

Dear users, I'm running NPT simulation POPC with a short peptide. I see the long bonds across the unit cell in VMD. Why am I getting broken lipid molecules in the trajectory (original .xtc file w/o any post-modification)? Some lipids move whole molecules, but some are broken. How can I control

Re: [gmx-users] image control

I'd suggest this is an issue with VMD rather than gromacs. You have to be quite careful which .gro you use to provide the original structure, make sure it is actually the starting frame and not anything else - this is something I've seen cause this sort of problem before. Normally, of course,

[gmx-users] interchain bond

Dear gromacs users, I have two identical peptides which should bind one metal ion. I guess I have not understood how I can make this bond. I labeled the two peptides with different chain identifier otherwise pdb2gmx does not understand that they are two peptides and not one protein. The metal

[gmx-users] Problems with GROMPP

I'd echo Justin's request for your *actual* commands. Computers are very literal, and we'd rather have your original commands than something that's clearly been filtered through your head. If the above reflects your actual use of wildcards on the command line, that sounds like a possible source

Re: [gmx-users] about parallel run

What i was trying to do is to run a parallel simulation. I have successfully compiled mdrun with mpi support. This is my grompp command grompp -f md.mdp -c rec_pr.gro -p rec.top -o rec.tpr -np 12 And this is the script I sent to the cluster: #!/bin/bash cd /home/yunierkis/MD export

Re: [gmx-users] image control

I don't think this is caused by VMD. The real coordinates of the part of the molicule in the .gro file (restart file from the end of simulation) will tell you. This means gromacs doesn't keep the whole molecule. Would you let me know what simulation setup you need for the cheking? I used

[gmx-users] about parallel run

What i was trying to do is to run a parallel simulation. I have successfully compiled mdrun with mpi support. This is my grompp command grompp -f md.mdp -c rec_pr.gro -p rec.top -o rec.tpr -np 12 And this is the script I sent to the cluster: #!/bin/bash cd /home/yunierkis/MD export

Re: [gmx-users] image control

Try using ngmx to visualise the simulation like I said, that'll tell you exactly what bonds gromacs thinks are there and definitively confirm whether there's a problem in the setup. Files that may have caused the problem are of course the obvious things like your mdp (what you've set pbc to,

Re: [gmx-users] Problems with GROMPP

I'd echo Justin's request for your *actual* commands. Computers are very literal, and we'd rather have your original commands than something that's clearly been filtered through your head. If the above reflects your actual use of wildcards on the command line, that sounds like a

Re: [gmx-users] image control

Thank you. First, I confirmed the broken lipid with ngmx. I did pbc = xyz, and I downloaded the popc.itp from Dr. Tieleman's homepage. [ bonds ] section in popc.itp is okay. Running MD is okay. (It doesn't crash; no extreme velocity) It's strange that some lipids around the boundary are kept in

Re: [gmx-users] dynamic cross correlation map

Hi, all: Does anybody know how to normalize the covariance matrix generated by g_covar with option -xpma. For -ascii, these data is the whole covariance matrix, which means the number in the matrix is 3N*3N (N is the number of atoms and I just choose alpha C). Now, I want to get the atomic

Re: [gmx-users] image control

Quoting Myunggi Yi [EMAIL PROTECTED]: I don't think this is caused by VMD. The real coordinates of the part of the molicule in the .gro file (restart file from the end of simulation) will tell you. This means gromacs doesn't keep the whole molecule. I have never known mdrun to write a broken

Re: [gmx-users] Go-model Hamiltonian

On Tue, 15 Jan 2008 08:20:05 -0600 eddie mendel [EMAIL PROTECTED] wrote: Greetings Gromax users! I am trying to do free energy calculations using a Go-model Hamiltonian simulation, and I was wondering if GROMACS has such capabilities. I was planning to use CHARMM but I found a problem at

Re: [gmx-users] interchain bond

On Tue, 15 Jan 2008 16:32:54 +0100 Velia Minicozzi [EMAIL PROTECTED] wrote: Dear gromacs users, I have two identical peptides which should bind one metal ion. I guess I have not understood how I can make this bond. I labeled the two peptides with different chain identifier otherwise pdb2gmx

Re: [gmx-users] image control

I didn't do any conversion. The gro file is restart file of the end of MD. On Jan 15, 2008 4:18 PM, Tsjerk Wassenaar [EMAIL PROTECTED] wrote: Hi Myunggi Yi, Did you by chance use trjconv prior to visualization? If so, what options did you use? mdrun doesn't write broken molecules. Cheers,

Re: [gmx-users] image control

Quoting Myunggi Yi [EMAIL PROTECTED]: On Jan 15, 2008 2:48 PM, Justin A. Lemkul [EMAIL PROTECTED] wrote: Quoting Myunggi Yi [EMAIL PROTECTED]: I don't think this is caused by VMD. The real coordinates of the part of the molicule in the .gro file (restart file from the end of

Re: [gmx-users] image control

Thank you all of you. I've got a pre-equilibrated hydrated POPC bilayer from a web-site. I made a hole, and I placed my protein. Now, what is the next step? On Jan 15, 2008 4:58 PM, Justin A. Lemkul [EMAIL PROTECTED] wrote: Quoting Myunggi Yi [EMAIL PROTECTED]: On Jan 15, 2008 2:48 PM,

Re: [gmx-users] image control

Myunggi Yi wrote: Thank you all of you. I've got a pre-equilibrated hydrated POPC bilayer from a web-site. I made a hole, and I placed my protein. Now, what is the next step? If you're asking this, then you'll want to read most of the links from this site

[gmx-users] how to create tpr file from pdb created with Hyperhem for using with OPLS

Dear Gromacs developers, I have some very simple questions on how to get the file (tpr) wich could be run on Gromacs (MD). With Hyperhem I have drawn the target molecule, I obtained ent file containing ATOM and CONNECT sections: 1) What should I change in this ent file to be able to run this

Re: [gmx-users] how to create tpr file from pdb created with Hyperhem for using with OPLS

Egidijus Kuprusevicius wrote: Dear Gromacs developers, I have some very simple questions on how to get the file (tpr) wich could be run on Gromacs (MD). With Hyperhem I have drawn the target molecule, I obtained ent file containing ATOM and CONNECT sections: 1) What should I change in this ent

Re: [gmx-users] image control

Thank you. I know general setup to run a simulation, and I'm running one. As you see the title, I have problem with image. I'm getting broken lipid in the trajectory. Would you let me know how to avoid this? Do I need special setup? On Jan 15, 2008 5:30 PM, Mark Abraham [EMAIL PROTECTED] wrote:

Re: [gmx-users] image control

Myunggi Yi wrote: Thank you. I know general setup to run a simulation, and I'm running one. As you see the title, I have problem with image. Well that was a dozen emails ago and we've talked about many topics since. You'll get nowhere fast by assuming that the people you're asking for help

[gmx-users] About g_msd

Hello again, I'm back with a few more questions about g_msd (version 3.3, in case I hadn't mentioned that before). Thanks to Xavier's message earlier, I have abandoned use of ordered trajectories to analyze my lipids. I will deal with lipid shells in the future. For now I am approaching the

Re: [gmx-users] About g_msd

What happens if you visualise the trajectory? Two orders of magnitude in scale of lipid movement should stick out like a sore thumb. - Original Message From: Justin A. Lemkul [EMAIL PROTECTED] To: gmx-users@gromacs.org Sent: Wednesday, January 16, 2008 12:27:45 AM Subject: [gmx-users]

Re: [gmx-users] About g_msd

Hi Alan, Thanks for the reply. My initial trajectory showed several of the lipids jumped across the box and continued through the bilayer from there, which resulted in a large displacement, so I processed the trajectory with trjconv -pbc nojump. There is still a rather large initial

[gmx-users] fatal errors in parallel but not on single processor

Hi, I'm new to gromacs and I can't figure out what I'm doing wrong with parallel runs. I'm running gromacs 3.3.2 on a 215 residue protein: 1rz4.pdb. The 2 missing residues were added with modloop followed by energy minimization. The protein was put in a dodecahedron box and solvated with a

[gmx-users] Re: gmx-users Digest, Vol 45, Issue 60

Thanks Mark, but your first answer didn't help me at all. I want to create pdb manually which will work with gromacs pdb2gmx comand in order to get gro and top using OPLS, and seeking for some clues. It doesn't matter if it is Hyperchem or JME or MOL, I need a proper pdb which will be

[gmx-users] N terminus charge groups in ffG53a6

Hi guys, I have a question about the assignment of charge groups at the N-terminus when applying the GROMOS 53a6 force field. But this may also be relevant to other force fields. When I run pdb2gmx (gmx 3.3.1) on a protein (lysozyme 1AKI in this case), it gives the following N terminus topology:

Re: [gmx-users] fatal errors in parallel but not on single processor

Patricia Francis-Lyon wrote: Hi, I'm new to gromacs and I can't figure out what I'm doing wrong with parallel runs. I'm running gromacs 3.3.2 on a 215 residue protein: 1rz4.pdb. The 2 missing residues were added with modloop followed by energy minimization. The protein was put in a

Re: [gmx-users] About g_msd

Justin A. Lemkul wrote: Hi Alan, Thanks for the reply. My initial trajectory showed several of the lipids jumped across the box and continued through the bilayer from there, which resulted in a large displacement, so I processed the trajectory with trjconv -pbc nojump. There is still a rather

Re: [gmx-users] N terminus charge groups in ffG53a6

van Bemmelen wrote: Hi guys, I have a question about the assignment of charge groups at the N-terminus when applying the GROMOS 53a6 force field. But this may also be relevant to other force fields. When I run pdb2gmx (gmx 3.3.1) on a protein (lysozyme 1AKI in this case), it gives the