Re: [gmx-users] Advice needed on choosing a VdW cutoff

Steven Kirk wrote: Hello, I would be very grateful for advice on the following system: Consider a pair of spherical macromolecules of diameter ~2.5 nm, arranged along an x-axis so that their centres of mass are 4nm apart, then centered in a 14 x 10 x 10 nm periodic box, so that the minimum d

Re: [gmx-users] coarse-grained model

Dongsheng Zhang wrote: Yang Ye, I am sorry to tell you I am not clear yet. Do you think I need to specify energygrps and corresponding energygrp_table? If so, then I got any error message. gp1 includes atom A, and gp3 includes atom A and B. Gromacs will complain that atoma has been in two gro

Re: [gmx-users] coarse-grained model

Yang Ye, I am sorry to tell you I am not clear yet. Do you think I need to specify energygrps and corresponding energygrp_table? If so, then I got any error message. gp1 includes atom A, and gp3 includes atom A and B. Gromacs will complain that atoma has been in two groups. Each group uses it ow

[gmx-users] A Better Question - OS X Config

Sorry all, Here is a better question having read the on-line manual. How do I modify the following BASH config files so I can gmx commands understood. (e.g. pass the "luck" command test). What is my if I'm running an intel iMAc OS 10.4? Guidance appreciated. **computer-2:/etc root# cat p

Re: [gmx-users] coarse-grained model

Don't worry about that. mdrun -tablep {tablep} will follow the scheme {tablep}_A_A.xvg, {tablep}_B_B.xvg ... {tablep} may be replaced by your own filename. Yang Ye Dongsheng Zhang wrote: Yang ye, Thank you very much. I have three different monomers in my system, so I have 6 different regula

[gmx-users] atomtype not found

when i am trying to generate *.tpr file for energy minimization, i am getting error that "atomtype NR not found!". my ligand.itp file has atomtype NR. i have generated this file through prodrg. how should i decide the atomtype? ___ gmx-users mailing lis

Re: [gmx-users] coarse-grained model

Yang ye, Thank you very much. I have three different monomers in my system, so I have 6 different regular VMDs and 6 different 1-4 interactions. Could you please tell me how to organize those table.xvg files? energygrps = gp1 gp2 gp3 gp4 gp5 gp6 ... gp12 energygrp_table = A A B B C C A B A C B C

Re: [gmx-users] coarse-grained model

mdrun -tablep Dongsheng Zhang wrote: Hello, GMX users, I have a coarse-grained model. Both 1-4 and regular vdw interaction are tabulated, but no electrostatic interaction. Since there is no entry for 1-4 interaction in energy_table. I am thinking to fool gromacs by treating 1-4 interactions as

[gmx-users] coarse-grained model

Hello, GMX users, I have a coarse-grained model. Both 1-4 and regular vdw interaction are tabulated, but no electrostatic interaction. Since there is no entry for 1-4 interaction in energy_table. I am thinking to fool gromacs by treating 1-4 interactions as electrostatic interactions, in other wor

Re: [gmx-users] RE: Bound oxygen molecule

Hi, I am working on dimeric hemoglobin, which has a bound oxygen molecule O2. When I convert pdb file to gro and top files by pdb2gmx it fails, since Gromacs does not recognize O2. I have checked the discussion list and this kind of question was asked once, however, I still have the couple que

Re: [gmx-users] Implemetation of the CHARMM27 ff into gromacs : managment of dihedral terms

Hello Mark, Thanks for your scripts. They are well commented and very easy to understand. Unfornunately, they don't work with my CHARMM parm files. It is probably a problem of format at the .par begining. I don't know well Perl but I think I can fix this. In the conversion made by Yuguang MU, ava

Re: [gmx-users] proper dihedrals

Those parameters should be in **bond.itp file, and you can use four atoms to define a dihedral angle. You can check ffoplsaabon.itp. I am confused by that note as well. On Tue, 2006-07-11 at 13:14 -0400, ARGYRIOS KARATRANTOS wrote: > Hi all, > > according to the manual the proper dihedrals ar

Re: [gmx-users] proper dihedrals

those are supposed to be in a parameters file. If not, look for some published paper about dynamics with a system that has those same atom sequences you listed. Maybe there's even a paper related you your actual research and it has the parameters you need.==Original message text

Re: [gmx-users] REMD

so, if i observe in md.log an exchange like: "Repl ex 012 x 3" for e.g. time step 1 that would convert into: "1 0 1 3 2" for remd.xvg. is that correct? the way you translate looks reasonable but I never used the version (?) you use so I won't be able to comment more. the

[gmx-users] proper dihedrals

Hi all, according to the manual the proper dihedrals are set, using in the topology file(top file) the inner two atoms of the dihedral. But how i can set the two following dihedrals, which have the same inner atoms C-O-C-H C-O-C-C but different external atoms, and of course different K values(KJ

Re: [gmx-users] REMD

> you do need this option (-demux) and the xvg file should hold N+1 columns > containing the correct permutation of replicas, e.g. > > time repl 0 1 2 3 ... > 0 0 1 2 3 > 1 1 0 2 3 > 2 1 2 0 3 > > and so on so, if i observe in md.log an exchange like: "Repl ex 0

[gmx-users] Advice needed on choosing a VdW cutoff

Hello, I would be very grateful for advice on the following system: Consider a pair of spherical macromolecules of diameter ~2.5 nm, arranged along an x-axis so that their centres of mass are 4nm apart, then centered in a 14 x 10 x 10 nm periodic box, so that the minimum distance between eith

Re: [gmx-users] REMD

hm, i want to produce one continuous trajectory from several trajectories, that are output from a REMD run. i could not find much information about this matter, but from what i read i gathered that one needs to reorder all the trajectories into a new one using the demux option in trjcat. as f

Re: Re: [gmx-users] REMD

On Tue, 11 Jul 2006, merc mertens wrote: >hm, i want to produce one continuous trajectory from several trajectories, >that are output from a REMD run. i could not find much information about this >matter, but from what i read i gathered that one needs to reorder all the >trajectories into a new

Re: Re: [gmx-users] REMD

hm, i want to produce one continuous trajectory from several trajectories, that are output from a REMD run. i could not find much information about this matter, but from what i read i gathered that one needs to reorder all the trajectories into a new one using the demux option in trjcat. as far

Re: [gmx-users] REMD

at the end of a REMD run in gromacs I have as many trajectories as replicas used for simulation. To produce one continuous trajectory trjcat was recommended in a previous message. Since it neither makes sense to simply concatenate all trajectories nor can one sort them by time, I suspect that

[gmx-users] REMD

Hello, at the end of a REMD run in gromacs I have as many trajectories as replicas used for simulation. To produce one continuous trajectory trjcat was recommended in a previous message. Since it neither makes sense to simply concatenate all trajectories nor can one sort them by time, I suspect

Re: [gmx-users] high initial temperature with low ref_T

Dongsheng Zhang wrote: Dear Mark, Do you have any idea what's wrong with my simulation? You can find the mdp file and the description how I set up my system at the bottom of this email. If you're trying to do vacuum simulations with infinite cutoffs and no periodicity, then the .mdp looks fi

Re: [gmx-users] Question about center-of-mass removal

Thank you so much, Berk. I deeply appreciate of your comments. Jae H. Park Original message >Date: Tue, 11 Jul 2006 09:04:19 +0200 >From: "Berk Hess" <[EMAIL PROTECTED]> >Subject: Re: [gmx-users] Question about center-of-mass removal >To: gmx-users@gromacs.org > > > > >>From: Jae H

Re: [gmx-users] Energy profile with umbrella sampling

From: "pim lists" <[EMAIL PROTECTED]> Reply-To: [EMAIL PROTECTED],Discussion list for GROMACS users To: gmx-users@gromacs.org Subject: Re: [gmx-users] Energy profile with umbrella sampling Date: Tue, 11 Jul 2006 07:48:09 +0200 On 7/10/06, [EMAIL PROTECTED] <[EMAIL PROTECTED]> wrote: From

Re: [gmx-users] Question about center-of-mass removal

From: Jae Hyun Park <[EMAIL PROTECTED]> Reply-To: Discussion list for GROMACS users To: Discussion list for GROMACS users Subject: Re: [gmx-users] Question about center-of-mass removal Date: Tue, 11 Jul 2006 00:27:55 -0500 Thank you, Mark. I have one more question for the confirmation. So,