[gmx-users] Differences in version 3.0 and 3.3

Dear all, I was running an NPT molecular dynamics simulation on a system of 6 protein strands. I am using Gromacs version 3.3 and for some specific purposes, I was only using version 3.0. Starting from the same input structure, forcefield (OPLS) and same run parameters, I noticed that the Cou

Re: [gmx-users] How to use g_energy after parellal mdrun

Hi Jochen, Thanks for your response. That was some syntax error, now I am getting only single .edr file. Is there any restriction in mdp file parameters while running it in parallel mode ? And, is it necessary to run energy minimization and position restraining before running final mdrun ? With T

[gmx-users] Re: trjconv error

> Message: 2 > Date: Wed, 27 Aug 2008 15:31:58 +0530 (IST) > From: [EMAIL PROTECTED] > Subject: [gmx-users] trjconv error > To: gmx-users@gromacs.org > Message-ID: <[EMAIL PROTECTED]> > Content-Type: text/plain;charset=iso-8859-1 > > Dear Tsjerk > > we have checked it., but of no use it giving some

Re: [gmx-users] Keeping portions of a protein fixed during energy minimization and MD simulations

shyamala iyer wrote: Hi all, I have a question regarding keeping certain protein residues fixed during EM and MD simulations. I wish to keep a portion of the protein fixed while minimizing the residues close to the ligand and ligand binding site. Is there a way to accomplish this? Create an

[gmx-users] Keeping portions of a protein fixed during energy minimization and MD simulations

Hi all, I have a question regarding keeping certain protein residues fixed during EM and MD simulations. I wish to keep a portion of the protein fixed while minimizing the residues close to the ligand and ligand binding site. Is there a way to accomplish this? Thanks, Shyamala Iyer Department o

Re: [gmx-users] Re: gmx-users Digest, Vol 52, Issue 97 (Justin A. Lemkul)

I figured out the problem. You have nucleotides in your aminoacids.dat file, don't you? For anyone who comes across this thread, have a look here: http://chemistry.csulb.edu/ffamber/#usage If nucleic acid names are included in aminoacids.dat, an incorrect topology is produced, requiring a ma

[gmx-users] Re: gmx-users Digest, Vol 52, Issue 97 (Justin A. Lemkul)

Hello Justin. I know I just sent you an email in reply to your last one, but now things seemed to have finally worked out. What I did was simply to add a Cytidine residue to the 5' end and a Guanine to the 3' end of each chain. Now all of a sudden I have integer charge and everything seems to work

Re: [gmx-users] Re: gmx-users Digest, Vol 52, Issue 97

Ragnarok sdf wrote: Hello Justin. You asked about adding solvents or ions. Well I added solvent to the box using genbox, but the non integer total charge comes from the beggining of the proccess, directly from pdb2gmx. Ions didn't have the chance to get to that part, since my grompp command g

[gmx-users] error ffg53a and thanks

Dear justin mer30.and thanks .you are great.I do it as you tell me.and work. best wishes sh-karbalaee ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.or

[gmx-users] Re: gmx-users Digest, Vol 52, Issue 97

Hello Justin. You asked about adding solvents or ions. Well I added solvent to the box using genbox, but the non integer total charge comes from the beggining of the proccess, directly from pdb2gmx. Ions didn't have the chance to get to that part, since my grompp command gives out error about bond

Re: [gmx-users] How to use g_energy after parellal mdrun

vivek sharma wrote: Hi There, I am running gromacs in a parellel architecture using -np 20. Now I want to generate the energy plot using g_energy, but there are 20 .edr files. Really? I get only one ener.edr, even in parallel mode. Or did you use -multi? Jochen How should I use the g_ene

Re: [gmx-users] when gen_vel should be "no"

sarbani chattopadhyay wrote: hi, I want to know that in what situation does the initial velocity to the starting structure is to be kept at zero. Please note that you may want to use the velocities in a gro file as starting velocities. In that case, you must use gen_vel = no, otherwise

Re: [gmx-users] Re: gmx-users Digest, Vol 52, Issue 97

Have you done anything else to your structure like adding solvent and ions? I'm betting that's where this error is coming from. Check the .itp files produced by pdb2gmx - the last line in the [ bonds ] section will give you a qtot (total charge) for each molecule. If all of these values are n

Re: [gmx-users] error ffg53a

shahrbanoo karbalaee wrote: Dear justin as you wrote, the first I make tfe.topology with this force field by command pdb2gmx and pdbfile from prodrg.and add to box with spc.now I have the file spc and tfe.by command grommp I minimized this file .I got a file emsolve.after this ,I work on th

[gmx-users] error ffg53a

Dear justin as you wrote, the first I make tfe.topology with this force field by command pdb2gmx and pdbfile from prodrg.and add to box with spc.now I have the file spc and tfe.by command grommp I minimized this file .I got a file emsolve.after this ,I work on this peptide . pdb2gmx -f name -

[gmx-users] RE: g_mindist option

Hi Alka, >So according to the header information the third column (all >0.00) is the information for maximum internal distance but i >am not getting what it conveys. >From the manual of g_mindist (http://www.gromacs.org/documentation/reference/online/g_mindist.html): "It also plots the maximum

[gmx-users] Re: gmx-users Digest, Vol 52, Issue 97

> > Hello Justin, sorry for the delay but I was trying repeat all my steps once > more so that I was sure that the error would come out the same. It did. Here is a part of my itp file: ; ;File '1vkxdna_A.itp' was generated ;By user: onbekend (0) ;On host: onbekend ;At date: Wed Aug

Re: [gmx-users] when gen_vel should be "no"

On 27.08.2008, at 11:14, sarbani chattopadhyay wrote: hi, I want to know that in what situation does the initial velocity to the starting structure is to be kept at zero. thanks in advance sarbani Hello, I think generating no initial vel. prevents introducing an artificial curre

Re: [gmx-users] error ffg53a5

Alright, you've sent two .top files and an .itp file, which is only mentioned in one of the .top files. If you want free help, make it easy to understand :) How are you using each of these topologies? I don't know how to reconstruct what you're trying to do. Which of these .top files gives

[gmx-users] error ffg53a5

Dear justin here it is .the files is attached.I insert gd-29 in line before the last line (dehidral) so . best -- sh-karbalaee ; ; File 'topol.top' was generated ; By user: onbekend (0) ; On host: onbekend ; At date: Thu Aug 21 23:30:46 2008 ; ; This is your topology

Re: [gmx-users] trjconv error

Hi, > we have checked it., but of no use it giving some error., > for your kind information, this "trjconv_mpi" command works for a protein > with a drug molecule, a protein moleclue, a dimer, etc.. So it's not trjconv_mpi, it's the trajectory that's wrong. Could you give the directory listing? (

[gmx-users] Re: Help

vivek sharma wrote: HI justin, Thanks for reply. It is well understood that the energy minimization step will minimize energy, but what is the purpose of MD (after EM and PR)? please reply Again, please keep all Gromacs-related correspondence on the gmx-users list. The purpose of MD? Inte

[gmx-users] trjconv error

Dear Tsjerk we have checked it., but of no use it giving some error., for your kind information, this "trjconv_mpi" command works for a protein with a drug molecule, a protein moleclue, a dimer, etc.. but it gives out error only for a dimer with a drug complex., its really a mystery., if i am ma

Re: [gmx-users] Error with LINC warning

There are several hundred posts about LINCS warnings in the list archive that should provide a starting point. Also have a look here: http://wiki.gromacs.org/index.php/Errors#LINCS.2FSETTLE.2FSHAKE_warnings -Justin vivek sharma wrote: Hi there, I am running gromacs in parellel with mpi inte

Re: [gmx-users] ffg53a5

Please post your .top and tfe.itp. -Justin shahrbanoo karbalaee wrote: Dear justin I cannot find my error.I make mix solvent tfe and spc ( was minimized)and solvate on a peptide.I use ffg53a5 .I take this error .I saw in line 61 in top file but there is not Ho in top file and rtp file ffg53

[gmx-users] Error with LINC warning

Hi there, I am running gromacs in parellel with mpi interface..(np 20) but it is exiting with the following error in output file . . . .Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: max 1.151530 (between atoms 2685 and 2686) rms 0.187095 bonds that rotated more than

Re: [gmx-users] when gen_vel should be "no"

sarbani chattopadhyay wrote: hi, I want to know that in what situation does the initial velocity to the starting structure is to be kept at zero. Zero velocity corresponds to 0 K. If you're wondering when you should have gel_vel = yes versus gen_vel = no, think about what that param

[gmx-users] Re: Help

vivek sharma wrote: Hi Justin, I think my query is very basic regarding GROMACS, so I am mailing you individually instead of using mailing list. Basic or not, please keep all Gromacs-related correspondence on the gmx-users list. My query is ... How does gromacs proceed ? On what basis (pa

[gmx-users] G_SDF if reference atoms are in different residues

Dear Users, I want to calculate the spatial distribution function of lipid headgroups around a protein residue. Because I am using a coarse-grained model each 'residue' is a single CG particle. This means that when defining the 3 reference groups that define the local coordinate axes I have no

[gmx-users] when gen_vel should be "no"

  hi, I want to know that in what situation does the initial velocity to the starting structure is to be kept at zero. thanks in advance sarbani___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users

Re: [gmx-users] Corrupt TRR file -- skipping a bad frame?

Hi Matt, You can determine the size of a single frame in bytes from what you have and use 'split' to split up your corrupt trajectory. Now the corrupt frame may not have the correct size, so you'll probably have to think of a way to start splitting from the end. Cheers, Tsjerk On Wed, Aug 27, 2

Re: [gmx-users] ffg53a5

Hi sh-karbalaee, Do you have some .itp files you include? Can you track 'HO' in there? If all else fails, write out the full (preprocessed) topology file, using the option -pp of grompp and search there (although I'd still bet it's in one of the .itp files). Cheers, Tsjerk On Wed, Aug 27, 2008

Re: [gmx-users] trjconv error

Hi Parthiban and Sundar, Did you check the .trr file with gmxcheck? By the way, is this still that same (faulty) trjconv of these sysadmins of yours who compiled it with gcc 4.x? Cheers, Tsjerk On Wed, Aug 27, 2008 at 8:36 AM, <[EMAIL PROTECTED]> wrote: > hi all > > i can able to get .trr fi

Re: [gmx-users] Re: Re:Re:g_mindist option

Hi Alka, This list is not for posing riddles and puzzles, although they may be interesting ;) You should give all relevant information, or think carefully yourself. Actually, it may be helpful to reformulate your riddle and let you think about it... :p If your cubic box has dimensions of 6 nm an

[gmx-users] Re: Re:Re:g_mindist option

Thanks a lot for your reply Actually "maximum internal distance" is not a separate concept it is what i am getting in the mindist.xvg file shown below This is the mindist.xvg file: @ title "Minimum distance to periodic image" @xaxis label "Time (ps)" @yaxis label "Distance (nm)" @TY