Re: [gmx-users] Re: comparison of gromacs in CENTOS and UBUNTU

Alexandre Suman de Araujo wrote: Obviously the HD space has nothing to do with GMX performance (unless it is full, of course), but the use of Ubuntu precompiled packages can affect drastically the GMX performance, especially if you are also using pre-compiled MPI library package. An important

[gmx-users] problem with topolbuild execution

Hello I am trying to generate a .itp file of a Fe4S4 cluster from mol2 file with the help of topolbuild1_2_1 programm but a error is comming during execution stating Illegal characters for size information line. I dont know what is wrong with the input file. I am giving here the input mol2 file

[gmx-users] Re: genconf

Payman, Such little charge cannot produce large energies, so it seems you should run EM first and everything will be OK with your simulation. As far as understand non-zero charge is a resuts of averaging errors (during grompp!), you cannot remove this warning. ~ Vitaly On Wed, Jul 22, 2009 at

Re: [gmx-users] Re: genconf

Vitaly V. Chaban wrote: Payman, Such little charge cannot produce large energies, so it seems you should run EM first and everything will be OK with your simulation. As far as understand non-zero charge is a resuts of averaging errors (during grompp!), you cannot remove this warning. That's

[gmx-users] first and second neighbours

Hi, Where May I find a Non-bonded interactions to be excluded (first and second neighbours). – Pair interactions (1-4 interactions) in Gromcas ? Thanks Luis Scott -- Prof. Dr. Luis Paulo Scott CMCC- Centro de Matemática, Computação e Cognição Universidade Federal do ABC Grupo de Pesquisa em

Re: [gmx-users] first and second neighbours

Luis Paulo wrote: Hi, Where May I find a Non-bonded interactions to be excluded (first and second neighbours). – Pair interactions (1-4 interactions) in Gromcas ? I don't understand the question. Thanks Luis Scott -- Prof. Dr. Luis Paulo Scott CMCC- Centro de Matemática, Computação e

RE: [gmx-users] genconf

Thanks a lot Mark! I will run the system for equilibration and then try to replicate it. I will keep you guys posted. Payman -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Mark Abraham Sent: July 21, 2009 11:01 PM To: Discussion

[gmx-users] Periodic Boundary Condition Issues

Hello, I am trying to analyze the trajectory of the estrogen receptor alpha in water. As you know, the ER is a dimer and as such when it approaches the boundary for the simulation one of the monomers jumps to the other side of my box and thus screws up any post simulation calculations that we

[gmx-users] trr and xtc

Dear all, I did a simulation of spce water and every thing seemed ok, when I did mdrun -s file.tpr -o file.trr -c file_out.gro -v -g file.log, I got a file.trr with zero size, but I have file.xtc that seems fine with VMD. I don't what happened here. Any idea? Also I looked at the box size from

Re: [gmx-users] Periodic Boundary Condition Issues

Cooper, David R wrote: Hello, I am trying to analyze the trajectory of the estrogen receptor alpha in water. As you know, the ER is a dimer and as such when it approaches the boundary for the simulation one of the monomers jumps to the other side of my box and thus screws up any post

Re: [gmx-users] trr and xtc

Jamie Seyed wrote: Dear all, I did a simulation of spce water and every thing seemed ok, when I did mdrun -s file.tpr -o file.trr -c file_out.gro -v -g file.log, I got a file.trr with zero size, but I have file.xtc that seems fine with VMD. I don't what happened here. Any idea? What did

Re: [gmx-users] trr and xtc

Hi Justin, nstxout=0 nstvout=0 Pcoupl=berendsen Pcoupltype=isotropic In fact I used the mdp file of /tuto/water and I modified it for PME and v-rescale. But the rest is the same (I am using version 4.0.5) I finished the simulation but I saw file.trr is empty... the rest seems fine...even

Re: [gmx-users] trr and xtc

Jamie Seyed wrote: Hi Justin, nstxout=0 nstvout=0 Right, then the .trr file should be empty until the very end, when the last frame should be written. Like I said, probably a filesystem blip. Pcoupl=berendsen Pcoupltype=isotropic Note that all of your box vectors are the same at

Re: [gmx-users] trr and xtc

Thank you Justin, But how I can prevent from that (filesystem blip) to happen. Also May I change Pcoupl= Parrinello-rahman instead of berendsen (has it any effect?? since I have changed Tcoupl=v-rescale instead of berendsen)? By the way there was a warning after doing grompp, it said unknown or

[gmx-users] Re: genconf

Payman, What system fo you try to simulate? How was the initial configuration generated? Did you do EM of the small box before using genconf? Anyway, try to decrease the time step (several orders) and start a small (~1000 steps) MD run. If you experience the overlaps of the particles it should

Re: [gmx-users] Peptide - DMPC membrane simulations - Unstable system

Hi Justin, So after struggling through ... I have confirmed that the error was due to Gromacs version incompatibility. Now my simulation is past problematic step and continues running without any error. Also I am following your advice and also doing the same simulation but with two equilibration

[gmx-users] Re: trr and xtc

Jamie, To have a trajectory in TRR you should just change nstxout=0 nstvout=0 to non-zeros. -- Vitaly V. Chaban, Ph.D. (ABD) School of Chemistry V.N. Karazin Kharkiv National University Svoboda sq.,4, Kharkiv 61077, Ukraine email: cha...@univer.kharkov.ua,vvcha...@gmail.com skype:

Re: [gmx-users] Peptide - DMPC membrane simulations - Unstable system

Kirill Bessonov wrote: Hi Justin, So after struggling through ... I have confirmed that the error was due to Gromacs version incompatibility. Now my simulation is past problematic step and continues running without any error. Also I am following your advice and also doing the same

[gmx-users] Missing G53A6 parameters

Hello everyone. I'm trying to do a simulation with the 53A6 parameters of a molecule that contains a sulfur atom bonded to a CH1 atom and a nitrogen atom. There are no bonded parameters (bond, angle, dihedral) for these combinations. Does anyone have any idea what I could do about that?

Re: [gmx-users] trr and xtc

Jamie Seyed wrote: Thank you Justin, But how I can prevent from that (filesystem blip) to happen. Also May I I know nothing about your filesystem, but sometimes these things happen randomly. Try re-running with nstxout at some value other than zero and see if you get a non-empty .trr

Re: [gmx-users] Missing G53A6 parameters

Michael McGovern wrote: Hello everyone. I'm trying to do a simulation with the 53A6 parameters of a molecule that contains a sulfur atom bonded to a CH1 atom and a nitrogen atom. There are no bonded parameters (bond, angle, dihedral) for these combinations. Does anyone have any idea what I

Re: [gmx-users] Missing G53A6 parameters

Michael McGovern wrote: Thanks a lot for the response. They are derived from spectroscopic data. You're saying I should find more spectroscopic data? For consistency with the force field, yes. Otherwise you'll have to have some compelling reason for reviewers as to why any QM

[gmx-users] using two different combination rules for the LJ potential

Hello, I am trying to simulate a system composed of two different molecules. I made the topology files for each of the two molecules and I did some tests to validate the force-field parameters for my system. I do have all the correct parameters for my system but it turns out that for the

[gmx-users] How to cap a peptide using pdb2gmx

Hi everybody I downloaded a pdb entry from RCSB and it comes with charged terminii, for example, the first aminoacid is ATOM  1  N   ASN A   1  -8.901   4.127  -0.555  1.00  0.00   N ATOM  2  CA  ASN A   1  -8.608   3.135  -1.618  1.00  0.00   C ATOM  3  C  

Re: [gmx-users] How to cap a peptide using pdb2gmx

Camilo Andrés Jimenez Cruz wrote: Hi everybody I downloaded a pdb entry from RCSB and it comes with charged terminii, for example, the first aminoacid is ATOM 1 N ASN A 1 -8.901 4.127 -0.555 1.00 0.00 N ATOM 2 CA ASN A 1 -8.608 3.135 -1.618

[gmx-users] residue-residue specific energy plots

Is there any utility/tool out there that can take an outputted GROMACS trajectory, and output the energies (electric potential, VDW, etc.) of all residue-residue specific interactions as a function of time?  The g_energy utility does not give me the data I want, and it will not even allow you to

Re: [gmx-users] residue-residue specific energy plots

Jonathan Reyles wrote: Is there any utility/tool out there that can take an outputted GROMACS trajectory, and output the energies (electric potential, VDW, etc.) of all residue-residue specific interactions as a function of time? The g_energy utility does not give me the data I want, and it

Re: [gmx-users] trr and xtc

Hi, On Wed, Jul 22, 2009 at 1:13 PM, Justin A. Lemkul jalem...@vt.edu wrote: Jamie Seyed wrote: Thank you Justin, But how I can prevent from that (filesystem blip) to happen. Also May I I know nothing about your filesystem, but sometimes these things happen randomly. Try re-running

RE: [gmx-users] genconf

Hello, I minimized the initial output (from another simulation) first; then I replicated it. This time, the minimization of the bigger box was done more easily! I ran an MD simulation with the bigger box and after 6 hours, it has not crashed yet. But, I have a question. When we replicate a box,

Re: [gmx-users] genconf

Payman Pirzadeh wrote: Hello, I minimized the initial output (from another simulation) first; then I replicated it. This time, the minimization of the bigger box was done more easily! I ran an MD simulation with the bigger box and after 6 hours, it has not crashed yet. But, I have a question.

[gmx-users] Zn parameterization

Hello, I am curious - is there anyway to see what assumptions were made when parameterizing the Zn 2+ ion? Was it tetrahedrally or octahedrally coordinated? With waters only or with imidazoles? Do the different force fields make different assumptions? Guidance appreciated. Regards,

Re: [gmx-users] Zn parameterization

Marc Charendoff wrote: Hello, I am curious - is there anyway to see what assumptions were made when parameterizing the Zn 2+ ion? Was it tetrahedrally or octahedrally coordinated? With waters only or with imidazoles? Do the different force fields make different assumptions? Guidance

Re: [gmx-users] using two different combination rules for the LJ potential

Ana West wrote: Hello, I am trying to simulate a system composed of two different molecules. I made the topology files for each of the two molecules and I did some tests to validate the force-field parameters for my system. I do have all the correct parameters for my system but it turns out

Re: [gmx-users] genconf

Payman Pirzadeh wrote: Thanks a lot Mark! I will run the system for equilibration and then try to replicate it. I will keep you guys posted. Obviously, equilibrating under PBC NPT will allow the box to change size to suit the system... PBC NVT won't, so you can end up with unsuitable