Re: [gmx-users] how to calculate g_sdf and ionic conductivity

naimah haron naimah wrote: Hello all Did anyone know how to 1) calculate g_sdf? Start with g_sdf -h. 2) ionic conductivity? Don't know. Look in manual 7.4, 8 and maybe Appendix D. Can I have the commands for that If you do some more of your own work and ask focussed questio

[gmx-users] gmx-users:Running gromacs on IBM cluster

Dear gmx-users, I have been trying to run gromacs on IBM cluster on multiple nodes using loadleveler script. Do I have to compile gromacs on individual nodes? What do I have to do to run it on multiple nodes? I get the following error message: llsetpenv: execve failed with rc=-1 and errno=2 10

Re: [gmx-users] g_rdf and number of atoms to include

On Wed, Oct 21, 2009 at 07:28, Enemark Soeren wrote: > Dear users, > > I would like to compare interactions between molecules by using RDF. I have > tried looking at glycine and water, and compare the following two > interactions: > > 1) between the amine hydrogen atoms in glycine and the o

[gmx-users] Box vector error

Dear All I am using GROMCS 3.3.1 version. I had started the simulation of protein in water with an octahedral box of dimension 9.76276 9.20449 7.97128 0.0 0.0 3.25425 0.0 -3.25425 4.60225. However after 25ns the simulation aborts with the following error: Fatal erro

[gmx-users] CMAP request

Dear Paer, Thank you very much for your reply. MTSSL is not a peptide, but it was parameterized by some other group and we are trying to use the parameters. They have used CMAP for MTSSL. So we also want to take into account the CMAP in our gromacs calculations. I am not much familiar with git

[gmx-users] Re: how to calculate g_sdf and ionic conductivity

their charge group I utilized the GROMACS-4.0.5. I have searched the maillist to find some similar posts but they can not yet cope with this issues. Could you give me some clues, please? Best wishes, Chaofu Wu, Dr. ___

Re: [gmx-users] Box vector error

Hi Prem, There is just something terribly wrong with your system if it goes flat like that. But with only the information you give here, no one can tell you more than that. Cheers, Tsjerk On Wed, Oct 21, 2009 at 10:18 AM, Prem Singh Kaushal wrote: > Dear All > >     I am using GROMCS 3.3.1 ver

RE: [gmx-users] g_rdf and number of atoms to include

Hi Omer, Thanks for your input. Let me reformulate my problem: I have glycine molecules in the form of zwitterions: 1ZGLY N1 0.560 0.337 0.388 -0.0759 -0.2488 -0.5471 1ZGLYH12 0.625 0.312 0.461 0.6035 0.5922 -0.4315 1ZGLYH23

Re: [gmx-users] Coarse-Grain: GROMACS bond information to VMD

> Justin A. Lemkul wrote: >> >> I have also added a Perl script to the GROMACS site (the VMD page): >> >> http://www.gromacs.org/Developer_Zone/Programming_Guide/VMD >> >> The user provides an input topology file, and a .psf file is written, >> which can be loaded as data for the structure in VMD.

Re: [gmx-users] Re: how to calculate g_sdf and ionic conductivity

--- > > Message: 4 > Date: Wed, 21 Oct 2009 10:31:49 +0800 > From: wuxiao > Subject: [gmx-users] Fatal error: 2 particles communicated to PME node > 0 are more than a cell length out of the domain decomposition cell of > their charge group > To: > Message-ID: >

[gmx-users] Re: CMAP request

Hi Paer, Thank you very much for your mail. Here is the paper from where we are taking the MTSSL parameters J. Phys. Chem. B 2008 112, 5755-5767, by B. Roux and the supplementary in it. Thank you. Sudip Pär Bjelkmar wrote: Hi, 21 okt 2009 kl. 10.59 skrev Sudip Roy: Thank you very much

[gmx-users] mdp file

Hi I want to creat mdp file for energy minimization (em.mdp). if I want to minimize my system (pr+dna), by steepest descent and conjugate gradient such as for example 100 steps by steepest descent and 100 steps by conjugate gradient, how I can creat mdp file? _

[gmx-users] pdb file

my pdb file for dna and protein contains 640 and 1130 atoms respectively. if I want creat a new pdb file for studying pr-dna interaction, should be numbering and order of numbers changed? how? ___ gmx-users mailing listgmx-users@gromacs.org http://lis

Re: [gmx-users] mdp file

leila karami wrote: Hi I want to creat mdp file for energy minimization (em.mdp). if I want to minimize my system (pr+dna), by steepest descent and conjugate gradient such as for example 100 steps by steepest descent and 100 steps by conjugate gradient, how I can creat mdp file? For exampl

Re: [gmx-users] Box vector error

I tried to restart simulation, going back, from the time point where there was no substantial change in the dimensions of the box, but simulations aborts again after some time with the same error. The time points at which simulation aborts are random. Having simulated for 25ns now i do not want t

[gmx-users] Protein Solvent Dynamics - Coordinates for docking

Dear Gromacs Users, I have performed a protein in solvent simulation for 1 ns, the got the output files as: md_0_1.cpt md_0_1.edr md_0_1.gro md_0_1.log md_0_1.tpr md_0_1.trr md_0_1.xtc. I am following Justin Tutorial. Can anybody tell me how to extract the coordinates ? of the simulated prot

Re: [gmx-users] gmx-users:Running gromacs on IBM cluster

Nkwe Monama wrote: Dear gmx-users, I have been trying to run gromacs on IBM cluster on multiple nodes using loadleveler script. Do I have to compile gromacs on individual nodes? What do I have to do to run it on multiple nodes? That will depend how what your cluster is and how it is set up t

[gmx-users] mdp file

dear Mark thanks for your attention. is this mdp file true for energy minimization (100 steps by steepest descent and 100 steps by* conjugate gradient*)? define= -DFLEX_SPC constraints = none *integrator = steep nsteps = 100 integrator =

Re: [gmx-users] Protein Solvent Dynamics - Coordinates for docking

ram bio wrote: Dear Gromacs Users, I have performed a protein in solvent simulation for 1 ns, the got the output files as: md_0_1.cpt md_0_1.edr md_0_1.gro md_0_1.log md_0_1.tpr md_0_1.trr md_0_1.xtc. I am following Justin Tutorial. Can anybody tell me how to extract the coordinates ? of t

Re: [gmx-users] mdp file

leila karami wrote: dear Mark thanks for your attention. is this mdp file true for energy minimization (100 steps by steepest descent and 100 steps by/ conjugate gradient/)? define= -DFLEX_SPC constraints = none *integrator = steep nsteps = 1

Re: [gmx-users] how to mimick explicit hydrogen bonding

Hi Mark, Thanks for your answer. Mark Abraham ha scritto: > There's nothing directional about the physics of a hydrogen bond, unless > your model makes it so. There'd be nothing intrinsically valid or > invalid with that either, so long as you parameterized the force field > under that assumption

Re: [gmx-users] Protein Solvent Dynamics - Coordinates for docking

Dear Mark, Thanks for the advice and suggestions. I have used trjconv command as in the justin tutorial (trjconv -s md_0_1.tpr -f md_0_1.xtc -o md_0_1_noPBC.xtc -pbc mol -ur compact), but when i loaded the md_0_1.gro followed by md_0_1_noPBC.xtc in VMD, i could not see the protein jumping out of

[gmx-users] pdb file

my pdb file for dna and protein contains 640 and 1130 atoms respectively. if I want creat a new pdb file for studying pr-dna interaction, should be numbering and order of numbers changed? how? ___ gmx-users mailing listgmx-users@gromacs.org http://lis

Re: [gmx-users] Coarse-Grain: GROMACS bond information to VMD

HI all, I have try the top2psf.tcl from Justin and the top2psf.pf from the VMD website. But both of them can only deal with single chain system. Take an example, if there are 10 proteins (+water) in my system,  how to convert to topology of the total system to .psf file? I tried to append the

[gmx-users] energy minimization with position restraint

how can I do energy minimization with position restraint. how I creat cooresponding mdp file? what should considered except what is seen in below mdp file. define= -DPOSRES constraints = none integrator = steep nsteps = 100 emtol=

Re: [gmx-users] Coarse-Grain: GROMACS bond information to VMD

Baofu Qiao wrote: HI all, I have try the top2psf.tcl from Justin and the top2psf.pf from the VMD website. But both of them can only deal with single chain system. Take an example, if there are 10 proteins (+water) in my system, how to convert to topology of the total system to .psf file? I

RE: [gmx-users] energy minimization with position restraint

Apart from specifying -DPOSRES in your mdp file, you need to make sure that posre.itp will be included into your topology. There is usually a statement like 'ifdef POSRES ..." Andreas --- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf

Re: [gmx-users] Protein Solvent Dynamics - Coordinates for docking

ram bio wrote: Dear Mark, Thanks for the advice and suggestions. I have used trjconv command as in the justin tutorial (trjconv -s md_0_1.tpr -f md_0_1.xtc -o md_0_1_noPBC.xtc -pbc mol -ur compact), but when i loaded the md_0_1.gro followed by md_0_1_noPBC.xtc in VMD, i could not see the prot

Re: [gmx-users] pdb file

leila karami wrote: my pdb file for dna and protein contains 640 and 1130 atoms respectively. if I want creat a new pdb file for studying pr-dna interaction, should be numbering and order of numbers changed? how? Numbering is the least of your worries, generating a reasonable starting str

Re: [gmx-users] energy minimization with position restraint

leila karami wrote: how can I do energy minimization with position restraint. how I creat cooresponding mdp file? what should considered except what is seen in below mdp file. Reading the manual, wiki, and the many tutorials available will give you the background you need. The obvious qu

Re: [gmx-users] Coarse-Grain: GROMACS bond information to VMD

Hi, All TCL scripts dowloaded from the VMD website as well as mine are supposed to be used within VMD. You have to run VMD first, then source the script. Alternatively, you can source it in your .vmdrc file. After that, you can run the g_cg function Nicolas > > > > > > > > HI all, >

Re: [gmx-users] Protein Solvent Dynamics - Coordinates for docking

Dear Justin, Thanks for the suggestion and advice. As i have used a modelled protein and want to obtain the lowest energy configuration of the protein by doing dynamics, i want to collect the structure (coordinates in pdb) representing average of all the frames/configurations produced in MD and al

Re: [gmx-users] scripts to generate topology CG

There is a seq2itp.pl script provided by martini folks in their website. You can get it from there. Sunny On Wed, Oct 21, 2009 at 9:42 AM, Francesco Pietra wrote: > Hi: > I am looking for scripts that generate topology in coarse grained. > Thanks for indications. > > francesco pietra > _

[gmx-users] scripts to generate topology CG

Hi: I am looking for scripts that generate topology in coarse grained. Thanks for indications. francesco pietra ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://ww

Re: [gmx-users] Protein Solvent Dynamics - Coordinates for docking

ram bio wrote: Dear Justin, Thanks for the suggestion and advice. As i have used a modelled protein and want to obtain the lowest energy configuration of the protein by doing dynamics, i want to collect the structure (coordinates in pdb) representing average of all the frames/configurations pr

Re: [gmx-users] Protein Solvent Dynamics - Coordinates for docking

Dear Justin. Thanks for the suggestion, definitely i would run next time for a longer time 2-10 ns. Here, I want to learn the analysis part of the mdrun, In order to locate the lowest energy frame I executed command g_energy -f md_0_1.edr -o PE.xvg and the output was Statistics over 51 steps

Re: [gmx-users] Protein Solvent Dynamics - Coordinates for docking

ram bio wrote: Dear Justin. Thanks for the suggestion, definitely i would run next time for a longer time 2-10 ns. Here, I want to learn the analysis part of the mdrun, In order to locate the lowest energy frame I executed command g_energy -f md_0_1.edr -o PE.xvg and the output was Statistic

[gmx-users] Re: Chloroform (CHCl3) solvent box for G53a5 force field

OK, I started over with the CHCl3 box from scratch. I prepared the following itp file from the CHCL3 parameters in ffG53a5.rtp: ---[chcl3.itp]--- [ moleculetype ] ; Namenrexcl CHCL3 3 [ atoms ] ; nr type resnr residue atom cgnr charge mass 1

Re: [gmx-users] Protein Solvent Dynamics - Coordinates for docking

Dear Justin, Thanks for the advice, will try to follow using grace. Ram On Wed, Oct 21, 2009 at 8:25 PM, Justin A. Lemkul wrote: > > > ram bio wrote: >> >> Dear Justin. >> >> Thanks for the suggestion, definitely i would run next time for a >> longer time 2-10 ns. >> Here, I want to learn the a

Re: [gmx-users] Re: Chloroform (CHCl3) solvent box for G53a5 force field

Pablo Englebienne wrote: OK, I started over with the CHCl3 box from scratch. I prepared the following itp file from the CHCL3 parameters in ffG53a5.rtp: ---[chcl3.itp]--- [ moleculetype ] ; Namenrexcl CHCL3 3 [ atoms ] ; nr type resnr residue atom cgnr

Re: [gmx-users] Coarse-Grain: GROMACS bond information to VMD

Hello everybody, Here is the rtf file I mentioned previously. It can be used by PSFGEN to generate a psf file from pdb files. The result can be used, for example, by the PME Electrostatics plugin of VMD. PSFGEN is available as a VMD plugin or as an independant executable. Nicolas Nicolas SA

[gmx-users] why the force is so large in energy minimization

I did a energy minimization on a system contain one [AuCl4]- and 503 water moleculars, by using a self-define non-bond interaction (which is obtain from ab-initio calculation), my em.mdp file is as follow: title  = yqq cpp    = /usr/bin/cpp ; the c pre-processor de

[gmx-users] alternative means of calculating PMF

Hello. I have finished calculating the PMF of dimerization for my system using umbrella sampling and WHAM. But came up with some free energy values that are not compatible to the ones found in other works. I have alread had several instrutions and tips from Justin in past email here in gms users' l

[gmx-users] alternative means of calculating PMF

Hi Stefan, If you know the bound state, you can use the double decoupling method to decouple the bound state and then recouple into bulk solvent. Note that both decoupling and umbrella sampling methods will require that you make the appropriate corrections to standard state values and tha

[gmx-users] PMF and g_wham

While using g_wham to obtain a PMF from umbrella sampling simulations I came up with the following problem. I have simulated my windows with a 0.1nm difference between structures starting from the initial position where my dimer is equilibrated and ending 0.5nm farther than what the lennard jones a

[gmx-users] Extended trajectory

Hi, I'll be most thankful if someone could tell me how to run a fragmented trajectory using only the mdrun command. As of now I'm using : while(SimuTime < SimTime) { ... system("tpbconv -s run.tpr -f run.trr -e run.edr -extend 1.0 -o run.tpr"); system("mdrun -cpi run.cpt -cpo

Re: [gmx-users] Extended trajectory

Arik Cohen wrote: Hi, I'll be most thankful if someone could tell me how to run a fragmented trajectory using only the mdrun command. As of now I'm using : while(SimuTime < SimTime) { ... system("tpbconv -s run.tpr -f run.trr -e run.edr -extend 1.0 -o run.tpr"); system("md

Re: [gmx-users] Extended trajectory

Thanks allot for all your help Arik Justin A. Lemkul wrote: Arik Cohen wrote: Hi, I'll be most thankful if someone could tell me how to run a fragmented trajectory using only the mdrun command. As of now I'm using : while(SimuTime < SimTime) { ... system("tpbconv -s run.tpr

[gmx-users] COM removal type angular with PBC?

Dear All, I'm attempting to simulate a dimeric protein in an explicit bilayer/water environment. I'd like to remove the translation & rotation of one protomer relative to the other, so that one protomer is able to move around relative to the stationary one. I'm using semiisotropic pressure coupling

Re: [gmx-users] Protein Solvent Dynamics - Coordinates for docking

ram bio wrote: Dear Justin, Thanks for the suggestion and advice. As i have used a modelled protein and want to obtain the lowest energy configuration of the protein by doing dynamics, That's all very well, but what will that give you other than a set where the partition of total energy into

Re: [gmx-users] COM removal type angular with PBC?

jennifer johnston wrote: Dear All, I'm attempting to simulate a dimeric protein in an explicit bilayer/water environment. I'd like to remove the translation & rotation of one protomer relative to the other, so that one protomer is able to move around relative to the stationary one. I'm using s

Re: [gmx-users] why the force is so large in energy minimization

青 叶 wrote: I did a energy minimization on a system contain one [AuCl4]- and 503 water moleculars, by using a self-define non-bond interaction (which is obtain from ab-initio calculation), my em.mdp file is as follow: title = yqq cpp= /usr/bin/cpp ; the c pre

Re: [gmx-users] how to mimick explicit hydrogen bonding

ms wrote: Hi Mark, Thanks for your answer. Mark Abraham ha scritto: There's nothing directional about the physics of a hydrogen bond, unless your model makes it so. There'd be nothing intrinsically valid or invalid with that either, so long as you parameterized the force field under that assum

Re: [gmx-users] Coarse-Grain: GROMACS bond information to VMD

Baofu Qiao wrote: HI all, I have try the top2psf.tcl from Justin and the top2psf.pf from the VMD website. But both of them can only deal with single chain system. Take an example, if there are 10 proteins (+water) in my system, how to convert to topology of the total system to .psf file? I t

RE: [gmx-users] g_rdf and number of atoms to include

Omar's response answered that question on why they are different. In the first one you are grouping all three into one group, second is just one of the hydrogen types. The fact that the rdf you get is different indicates that all three hydrogens are not identical. Have you compared the rdf for e

[gmx-users] Setting up an infinitely hard wall

Hi everyone, I have been trying to set up an "infinitely" hard potential wall. I tried to use the available wall options and could not really get it to do what i needed. I wanted a steep repulsive potential but when i created that, the system was blowing up, reason being that it requires smaller t

RE: [gmx-users] g_rdf and number of atoms to include

Ahh, now I understand - sorry, Omer! In fact, I have compared all three single hydrogen RDFs and they are identical and also relatively smooth. Since, however, with 3 times more data points (all three hydrogen atoms taken together) I get a different RDF, would that indicate that I do not have e

Re: [gmx-users] g_rdf and number of atoms to include

Enemark Soeren wrote: Ahh, now I understand - sorry, Omer! In fact, I have compared all three single hydrogen RDFs and they are identical and also relatively smooth. Since, however, with 3 times more data points (all three hydrogen atoms taken together) I get a different RDF, would that in