Re: [gmx-users] how to use a new force field

Hi, Well, to *add* a new force field, summerizing and extending the replies given earlier, you edit the file FF.dat in the directory $GMXPATH/share/gromacs/top.This file looks like 11 ffG43a1 GROMOS96 43a1 force field ffG43b1 GROMOS96 43b1 vacuum force field ffG43a2 GROMOS96 43a2 force field (

[gmx-users] Error estimation from FEP

I have done FEP simulations and am trying to find a way to report the error related to the values of relative delta G found. I have simulated 20 windows each with an interval of lambda of 0.05. Then used -rerun option from mdrun to perform the same simulation with a lambda value of (lambda+0.05) an

Re: [gmx-users] (??? ????)

Andrew Voronkov wrote: Dear GROMACS users, we want to make a refinement of protein structure by distributed computing MD calculations. For this we need to make random initial coordinates generation for 100 of 100 ps trajectories. It is something like fold...@home strategy uses for folding, but

Re: [gmx-users] how to use a new force field

Thank you v. much for the replies. I will try to set that up. Amit On Tue, Sep 8, 2009 at 6:57 PM, Dallas B. Warren < dallas.war...@pharm.monash.edu.au> wrote: > Best if you don't mess with the ones that are installed. Set up your own > forcefield files in a local directory and edit those, GROM

RE: [gmx-users] how to use a new force field

Best if you don't mess with the ones that are installed. Set up your own forcefield files in a local directory and edit those, GROMACS scripts will then look in the local directory first, before going to the installed one. Catch ya, Dr. Dallas Warren Department of Pharmaceutical Biology Pharm

Re: [gmx-users] Using gromacs 4.0.5 built with FORTIFY_SOURCE feature

Hi, Thank you for the information, > The Fedora packages of GROMACS have been compiled with the default > Fedora build flags which include -Wp,-D_FORTIFY_SOURCE=2 and no such > problems have been encountered. This is both in Fedora 10 and 11, and in > RHEL 4 and 5. Well, This means FORTIFY_SOURC

Re: [gmx-users] how to use a new force field

Amit Choubey wrote: hi, ok the next question that bugs me is if i make a directory consisting of my modified force field (*.atp, *.rtp, *bon.itp,*nb.itp) and i want to use pdb2gmx to get the *.top & .gro files according to the above new FF files, how do i supply this info to pdb2gmx. In oth

Re: [gmx-users] how to use a new force field

By the way thank you very much for answering my questions. Amit On Tue, Sep 8, 2009 at 7:13 PM, Amit Choubey wrote: > hi, > ok the next question that bugs me is if i make a directory consisting of my > modified force field (*.atp, *.rtp, *bon.itp,*nb.itp) and i want to use > pdb2gmx to get the

Re: [gmx-users] how to use a new force field

hi, ok the next question that bugs me is if i make a directory consisting of my modified force field (*.atp, *.rtp, *bon.itp,*nb.itp) and i want to use pdb2gmx to get the *.top & .gro files according to the above new FF files, how do i supply this info to pdb2gmx. In other words how do i make pdb2g

Re: [gmx-users] Using gromacs 4.0.5 built with FORTIFY_SOURCE feature

Hi, Thanks for the reply, >> I now use gentoo linux with gcc 4.3.4, which has FORTIFY_SOURCE feature. >> >> When I built gromacs 4.0.5 with this gcc, every command, like grompp, >> pdb2gmx >> and so on, makes buffer overflow and stoppes immediately. > > Whatever FORTIFY_SOURCE does, either it is p

Re: [gmx-users] how to use a new force field

Amit Choubey wrote: Hi, so is it a good idea to edit the original gromacs files in top directory for introducing new force field or is there a way to compliment the existing FF files by a new file made by me? It is generally better to not mess with system-level force field files unless

Re: [gmx-users] how to use a new force field

Hi, so is it a good idea to edit the original gromacs files in top directory for introducing new force field or is there a way to compliment the existing FF files by a new file made by me? Amit On Tue, Sep 8, 2009 at 2:38 PM, Justin A. Lemkul wrote: > > > Amit Choubey wrote: > >> hi gromacs us

Re: [gmx-users] selecting two groups for average structure

David Crosby wrote: Hello, I'm sure there's a simple solution to this problem, so please bear with me... I'm attempting to generate an average structure from a trajectory and I'd like to have it pool two groups into the final structure. I work with a magnesium-coordinating integrase protein, s

[gmx-users] selecting two groups for average structure

Hello, I'm sure there's a simple solution to this problem, so please bear with me... I'm attempting to generate an average structure from a trajectory and I'd like to have it pool two groups into the final structure. I work with a magnesium-coordinating integrase protein, so my groups are 1: prote

Re: [gmx-users] do_dssp question

Kirill Bessonov wrote: I have used do_dssp program to analyze secondary structure during simulation of DMPC/DMPE. But I am not clear on installation of dssp. The program seems to work, I have set all the environmental variables so that dssp binary is seen in /home/DSSP directory, but I am no

[gmx-users] do_dssp question

I have used do_dssp program to analyze secondary structure during simulation of DMPC/DMPE. But I am not clear on installation of dssp. The program seems to work, I have set all the environmental variables so that dssp binary is seen in /home/DSSP directory, but I am not sure if I need to download

Re: [gmx-users] how to use a new force field

Amit Choubey wrote: hi gromacs user, Is there any good way to introduce new force field in the gromacs library? Read in the manual about the organization of existing force fields, as well as the component files that are necessary to make it function. Beyond that, look at the implemented

[gmx-users] how to use a new force field

hi gromacs user, Is there any good way to introduce new force field in the gromacs library? Amit ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/s

Re: [gmx-users] weird mdrun...using gromacs 3.3.3

Hi Justin, I tried "unconstrained_start = yes". It did not work. I freeze CNT, CMT groups rather than constraints. To try from scratch, I deleted all the groups apart from CNT and CMT, then solvated the box with water. I ran a short simulation for 5000 steps, it runs fine. But when I tried to res

Re: {Spam?} Re: [gmx-users] Re: wierd behavior of mdrun

This is not a Gromacs issue. You should take it up with your sysadmin. Perhaps you are seeing sporadic successes and failures due to a buggy node (or multiple!) or perhaps you have typos in your submission script. -Justin Paymon Pirzadeh wrote: OK! I tested your suggestion about frequent

Re: {Spam?} Re: [gmx-users] Re: wierd behavior of mdrun

OK! I tested your suggestion about frequent output. As you had predicted, it crashed immediately. But the message I got from the cluster was PBS Job Id: 94865.orca1.ibb Job Name: AFPIII_NVT275test job deleted Job deleted at request of r...@elder2.ibb MOAB_INFO: job was rejected - job violates

[gmx-users] (Без темы)

Dear GROMACS users, we want to make a refinement of protein structure by distributed computing MD calculations. For this we need to make random initial coordinates generation for 100 of 100 ps trajectories. It is something like fold...@home strategy uses for folding, but we want to get the traje

Re: [gmx-users] Using gromacs 4.0.5 built with FORTIFY_SOURCE feature

On Tue, 2009-09-08 at 21:11 +0900, Yasuyuki Araki wrote: > hi, > > I now use gentoo linux with gcc 4.3.4, which has FORTIFY_SOURCE feature. > > When I built gromacs 4.0.5 with this gcc, every command, like grompp, pdb2gmx > and so on, makes buffer overflow and stoppes immediately. > > I saw the

Re: [gmx-users] weird mdrun...using gromacs 3.3.3

Naga Rajesh Tummala wrote: I usually use the final output file generated by GROMACS which contain the velocity. But, I dont preserve the velocity every timestep. CNT, CMT are constrained. I would want to make them move only in X direction, but I cannot make the simulation work even when th

Re: [gmx-users] potential energy NaN and strange dependence on cut-offs

Manik Mayur wrote: 2009/9/8 Mark Abraham > Jennifer Williams wrote: Hi users, I am running a very simple simulation of methane inside a pore (v.much like a carbon nanotube but in my case the tube is supposed to represent sil

Re: [gmx-users] weird mdrun...using gromacs 3.3.3

> Can you post the relevant .mdp file(s)? Are you preserving velocity > information from the previous trajectory, or generating new velocities? Are > any of the species in your system constrained? > > -Justin > I usually use the final output file generated by GROMACS which contain the velocity.

Re: [gmx-users] potential energy NaN and strange dependence on cut-offs

2009/9/8 Mark Abraham > Jennifer Williams wrote: > >> Hi users, >> >> I am running a very simple simulation of methane inside a pore (v.much >> like a carbon nanotube but in my case the tube is supposed to represent >> silica.) I keep this tube frozen. >> >> I start with an energy minimisation-ho

Re: [gmx-users] weird mdrun...using gromacs 3.3.3

Naga Rajesh Tummala wrote: Dear Justin, The initial configuration for this simulation is the configuration obtained from 10 ns of simulation. The only thing that is changed is that I now consider a nanotube as a single rigid body connected by bonds, so that I can make the nanotube move alo

Re: [gmx-users] weird mdrun...using gromacs 3.3.3

Dear Justin, The initial configuration for this simulation is the configuration obtained from 10 ns of simulation. The only thing that is changed is that I now consider a nanotube as a single rigid body connected by bonds, so that I can make the nanotube move along the x-direction as a whole. I d

Re: [gmx-users] potential energy NaN and strange dependence on cut-offs

Jennifer Williams wrote: Hi users, I am running a very simple simulation of methane inside a pore (v.much like a carbon nanotube but in my case the tube is supposed to represent silica.) I keep this tube frozen. I start with an energy minimisation-however this runs to completion almost inst

Re: [gmx-users] Using gromacs 4.0.5 built with FORTIFY_SOURCE feature

Yasuyuki Araki wrote: hi, I now use gentoo linux with gcc 4.3.4, which has FORTIFY_SOURCE feature. When I built gromacs 4.0.5 with this gcc, every command, like grompp, pdb2gmx and so on, makes buffer overflow and stoppes immediately. Whatever FORTIFY_SOURCE does, either it is poorly-construc

[gmx-users] potential energy NaN and strange dependence on cut-offs

Hi users, I am running a very simple simulation of methane inside a pore (v.much like a carbon nanotube but in my case the tube is supposed to represent silica.) I keep this tube frozen. I start with an energy minimisation-however this runs to completion almost instantly and I keep get Na

[gmx-users] Using gromacs 4.0.5 built with FORTIFY_SOURCE feature

hi, I now use gentoo linux with gcc 4.3.4, which has FORTIFY_SOURCE feature. When I built gromacs 4.0.5 with this gcc, every command, like grompp, pdb2gmx and so on, makes buffer overflow and stoppes immediately. I saw the archives of this mailing list and found this situation was quite similar

Re: [gmx-users] weird mdrun...using gromacs 3.3.3

Naga Rajesh Tummala wrote: Dear Mark, Some groups which were constrained in all 3 dimensions in one .mdp whereas in other .mdp that groups were not constrained in x-direction. But now I used same .mdp file and now even "nrdf" are same. Strangely (common atleast when doing this simulation),

[gmx-users] long range restrain

Dear Colleagues, I am using gromacs 4.0.5, when I applied some long-ranged restrains (using NMR restrain tools), it stopped with output: Time or ensemble averaged or multiple pair distance restraints do not work (yet) with domain decomposition, use particle decomposition (mdrun option -pd) Howeve