[gmx-users] Re: Regarding error.

Dear Suryanarayana, This error itself tells you that the particular residue 'DAL' is not available in the residue topology database of the force field you are using for your simulation. You can check that by yourself in the *.rtp file of corresponding force field. The way out of this situation is

Re: [gmx-users] LINCS warning and segmentation fault for methane in 1-octanol simulation

= none ; turn off everything, in this case only vdW - Thanks, Vivek On 09/02/2012, Justin A. Lemkul jalem...@vt.edu wrote: vivek sharma wrote: Hi There, I was trying to run a equilibrium run (npt) for system of Methane in 1-octanol (1 methane molecule with 200 1-octanol molecules

[gmx-users] LINCS warning and segmentation fault for methane in 1-octanol simulation

be wrong with above simulation. Regards, Vivek Sharma -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests

[gmx-users] Error while running methane in water simulation

for the distortion in methane during simulation.* * Thanks and regards, *Vivek Sharma* -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un

Re: [gmx-users] Error while trying REMD on cluster

Thanks Justin for your advice, it was one of the mpi flags only which caused the error. regards, Vivek On 27 May 2011 17:39, Justin A. Lemkul jalem...@vt.edu wrote: vivek sharma wrote: HI GMX-users, I am trying to run a REMD simulation on my system. I have created 10 .tpr files

[gmx-users] Error while trying REMD on cluster

HI GMX-users, I am trying to run a REMD simulation on my system. I have created 10 .tpr files and fired the simulation using the following command - bsub -n 40 -o out_1 -e err_1 mpirun mdrun_d -s MD.tpr -multi 10 -replex 2 -o MD.trr -e MD.edr -g MD.log -c MD.gro

[gmx-users] Simulated annealing with implicit water model

Hi There, I am going to run a simulated annealing simulation on a system with implicit water model. I have tried running simulated annealing with explicit water model. Please suggest and comment if anybody have tried such simulation in gromacs. with thanks, Vivek -- gmx-users mailing list

[gmx-users] Error while compiling gromacs-4.5.4

Hi there, I am trying to install gromacs-4.5.4 on my local machine with FC, I tried following set of commands: -to install FFTW at location root/Desktop/Vivek/calcitonin/FFTW ./configure --prefix=/root/Desktop/Vivek/calcitonin/FFTW --enable-long-double make make

[gmx-users] Gromacs benchmarking results

76 89.534 I am looking for some more benchmarks on the same example set, to compare these results. Please, share if somebody has tried it. Expecting some helpful comments and suggestions to improve the performance further. Thanks, Vivek Sharma -- gmx-users mailing list

Re: [gmx-users] MD on docked complex using AMBER FF

to Gromacs topology. You will need AmberTools and a script called amb2gmx.pl. Following links would be helpful for you http://ambermd.org/#AmberTools http://ambermd.org/antechamber/efz.html ffamber.cnsm.csulb.edu/amb2gmx.pl On Tue, Sep 21, 2010 at 12:51 AM, vivek sharma viveksharma.i...@gmail.com

[gmx-users] MD on docked complex using AMBER FF

Hi There, I am trying to run molecular dynamics on a drug-enzyme complex using amber force field. I have done it earlier using gromos FF using drug-enzyme tutorial, I dont know if the parameter set (.mdp file) will be same or different while using AMBER FF. Any insight/comments into the matter may

[gmx-users] Lysozyme benchmarking for gromacs-4,0.5

Hi there, I am running a GROMACS benchmarking on my cluster with the Lysozyme example provided in benchmarking files. I am looking at ns/day to compare the performance of various runs. I am using gromacs-4.0.5, Can somebody provide me with the figures to compare the performance? Also DO I need to

[gmx-users] Gromacs-4 benchmarking

Hi There, I want to benchmark the scalability and speed for gromacs-4 on our cluster. I want to know if there is any benchmarking activity already goin on? I have browsed and got benchmarking for gromacs-3 and it seems that gromacs-4 is much more scalable and faster than gromacs-3. Can somebody

[gmx-users] Error while trying free energy calculation

Hi There, I was trying to run a free energy tutorial given at * http://www.dillgroup.ucsf.edu/group/wiki/index.php?title=Free_Energy:_Tutorial * While trying the very first run i.e. mdrun using *min_lbfgs0.mdp* I ended up with following error ERROR: With coulombtype = PME,

Re: [gmx-users] Re: MD run for octanol system

Hi Esteban and Vitaly, Thanks for your respose, I tried trjconv with -pbc mol while generating movie and it worked this time. regards, vivek On 12 July 2010 16:01, Vitaly Chaban vvcha...@gmail.com wrote: Hmm... Straight lines... Is it VMD that your used to visualize the trajectory? I think

[gmx-users] MD run for octanol system

Hi There, I am trying to run MD simulation for octanol using GROMACS, I have downloaded the octanol.tar.gz from the user contributed section http://www.gromacs.org/@api/deki/files/18/=octanol.tar.gz. When I performed this MD run according to the run input file and molecule topology provided in

Re: [gmx-users] Ligand coming out while trying Drug-enzyme tutorial

, Tsjerk On Wed, Jan 27, 2010 at 5:58 AM, vivek sharma viveksharma.i...@gmail.com wrote: Hi Dallas, I am trying to run MD simulation over a docked complex (protein+ligand), to confirm their dynamic stability in water media. For the same I am using PRODRG server to generate topologies

Re: [gmx-users] Ligand coming out while trying Drug-enzyme tutorial

to come out of this problem. Thanks Regards, Vivek On 27 January 2010 10:40, Mark Abraham mark.abra...@anu.edu.au wrote: On 27/01/10 15:58, vivek sharma wrote: Hi Dallas, I am trying to run MD simulation over a docked complex (protein+ligand), to confirm their dynamic stability in water

Re: [gmx-users] Ligand coming out while trying Drug-enzyme tutorial

Of *vivek sharma *Sent:* Monday, 25 January 2010 7:38 PM *To:* Discussion list for GROMACS users *Subject:* Re: [gmx-users] Ligand coming out while trying Drug-enzyme tutorial HI Tsjerk, Thanks for your reply. But, I can't see if it is going suddenly or gradually. What i can see is the ligand

Re: [gmx-users] Ligand coming out while trying Drug-enzyme tutorial

HI Tsjerk, Thanks for your reply. But, I can't see if it is going suddenly or gradually. What i can see is the ligand is away from the molecule after editing the gro file with PRODRG output. It seems liek PRODRG has modified the co-ordinates that places ligand away from the protein. ~Vivek

[gmx-users] Ligand coming out while trying Drug-enzyme tutorial

Hi All, I was trying *GROMACS Tutorial for Drug – Enzyme Complex* by *John E. Kerrigan* over one docked complex in following way. I generated topology and gromacs co-ordinates for ligand and cofactor successfully using PRODRG beta. Protein file is processed through pdb2gmax_d and resulted .gro

[gmx-users] Fatal error: No such moleculetype Na

Hi All, I am trying to run the tutorial http://code.google.com/p/acpypi/wiki/TutorialAcpypi4Gromacs; for using ACPYPI generated topology with GROMACS. I am using amber99sb forcefield for one docked complex. It is running successfully upto genion and giving error while doing grompp for energy

Re: [gmx-users] Optimizing a parallel simulation

Hi Mark, Thanks for your quick response. 2009/10/8 Mark Abraham mark.abra...@anu.edu.au vivek sharma wrote: Hi There, While running a parallel MD simulation, I got following message while playing with parameters: NOTE 3 [file aminoacids.dat, line 1]: The optimal PME mesh load

[gmx-users] Optimizing a parallel simulation

Hi There, While running a parallel MD simulation, I got following message while playing with parameters: NOTE 3 [file aminoacids.dat, line 1]: The optimal PME mesh load for parallel simulations is below 0.5 and for highly parallel simulations between 0.25 and 0.33, for higher performance,

[gmx-users] Error while scaling mdrun for more number of nodes.

Hi There, I was trying to rum mdrun on large number of nodes. When I tried the run on 57 nodes, I got an error which is pasted below. --- Program mpi_mdrun_d, VERSION 4.0.3 Source code file: domdec_setup.c, line: 147 Fatal error: Could not find

[gmx-users] x2top_d running for too long

Hi All, I am trying to generate the topology file for some molecule using x2top_d. I have fired the command as: *x2top_d -f Bromo-WR99210.pdb -o Bromo-WR99210.top -r Bromo-WR99210.rtp *This is executing from last 16 hours, I dont know whether it takes this much time or is there any problem

Re: [gmx-users] x2top_d running for too long

Hi Mark, Thanks for your reply. But I didn't got what does it mean? 2009/6/10 Mark Abraham mark.abra...@anu.edu.au vivek sharma wrote: Hi All, I am trying to generate the topology file for some molecule using x2top_d. I have fired the command as: */x2top_d -f Bromo-WR99210.pdb -o Bromo

[gmx-users] Packages for building topologies

Hi All, I was doing some MD simulation over the docked complex and following the drug-enzyme tutorial for the same. The tutorial provided by Kerrigan's is really helpful. Only problem with the tutorial is generating topologies, for which PRODRG server is suggested. I want to use some stand alone

Re: [gmx-users] Installing topolbuild

Hi Bruce, I was trying to generate topologies for one ligand using topolbuild. For the same I used the command *topolbuild -dir /home/vivek/topolbuild1_2_1/dat/gromacs/ -ff gmx43a1 -n Bromo-WR99210 -r RESID* and it resulted in an error as follow: *Fatal error. Source code file: readmol2.c,

[gmx-users] multiple outputs in mdrun with gromacs-4.0.3

Hi There, I have upgraded my Gromacs version from 3.3 to 4.0.3. I am using it with mpi over 24 processor and 3 nodes (each node having 8 processor). I fired an energy minimization run. while doing do, I found multiple copies of output files (.edr, .gro, .trr) instead of single file. Following is

Re: [gmx-users] Installing topolbuild

1:47:28 AM, vivek sharma viveksharma.i...@gmail.com wrote: * * I am trying to Install topolbuild on my system, while doing so with the make file given in the topolbuild folder. but I end up with a list of error mentioned below: .. . . . .compare_FF.c:(.text+0x1285): undefined

[gmx-users] Installing topolbuild

Hi There, I am trying to Install topolbuild on my system, while doing so with the make file given in the topolbuild folder. but I end up with a list of error mentioned below: .. . . . .compare_FF.c:(.text+0x1285): undefined reference to `exp' compare_FF.c:(.text+0x12cc): undefined reference to

[gmx-users] settingparameters for energy minimization

Hi There, I am trying to do energy minimization of some protein molecule, and I have following queries for the same. 1. Can I define some RMSD tolerance, such that RMSD value of the molecule during the energy minimization will not vary more than some predefined value. 2. Which integrator is better

Re: [gmx-users] settingparameters for energy minimization

Hi justin, Thank you very much for your quick reply. I also want to know is there any other option than PRODRG to generate topology files for the non-standard residues ? As PRODRG server usually go down these days. With thanks, Vivek 2009/3/2 Justin A. Lemkul jalem...@vt.edu vivek sharma

[gmx-users] Segmentation fault during Simulated annealing for different groups

Hi All, I am trying to run simulated annealing for my protein + NDP kept in a water box. I want to vary the temperature for the NDP only and want to keep the constant temperature for rest of the system. for the same when tried with making two groups, one for NDP and other for rest of the

[gmx-users] Using double precision files with single precision version

Hi All, I had a few MD runs with double precision in gromacs, Can I use single precision version of gromacs to play with those files e.g making movie files and extracting h_bond information. I am afraid if it will affect my results. Please suggest With thanks, Vivek

[gmx-users] Calculating the time for existence of h-bond

Hi All, I am analyzing the h-bond information for a mdrun using g_hbond. Can I know the % of trajectory time for which a bond between particular residue was existing? If anybody have tried such option please suggest me a way to do so. With thanks, Vivek

Re: [gmx-users] Calculating the time for existence of h-bond

if there is such an option in the same. With thanks, Vivek 2008/11/20 Mark Abraham [EMAIL PROTECTED] vivek sharma wrote: Hi All, I am analyzing the h-bond information for a mdrun using g_hbond. Can I know the % of trajectory time for which a bond between particular residue was existing? If anybody

[gmx-users] Error while trying position restraint

Hi There, I am running a psition restraint mdrun. For the same I am selecting the part of the molecule surrounding my LIG, and restraining the rest of system for mdrun (using genpr).. As my system is protein in water, it is not allowing me to select a part of SOL for position restraint and rest

Re: [gmx-users] Gromacs 4 Scaling Benchmarks...

Hi Carsten, I have also tried scaling gromacs for a number of nodes but was not able to optimize it beyond 20 processor..on 20 nodes i.e. 1 processor per node.. I am not getting the point of optimizing PME for the number of nodes, is it like we can change the parameters for PME for MDS or

Re: [gmx-users] Gromacs 4 Scaling Benchmarks...

HI MArtin, I am using here the infiniband having speed more than 10 gbps..Can you suggest some option to scale better in this case. With Thanks, Vivek 2008/11/11 Martin Höfling [EMAIL PROTECTED] Am Dienstag 11 November 2008 12:06:06 schrieb vivek sharma: I have also tried scaling gromacs

Re: [gmx-users] Gromacs 4 Scaling Benchmarks...

Hi All, one thing I forgot to mention I am getting here around 6 ns/day...for a protein of size around 2600 atoms.. With Thanks, Vivek 2008/11/11 vivek sharma [EMAIL PROTECTED] HI MArtin, I am using here the infiniband having speed more than 10 gbps..Can you suggest some option to scale

Re: [gmx-users] Gromacs 4 Scaling Benchmarks...

2008/11/11 Justin A. Lemkul [EMAIL PROTECTED] vivek sharma wrote: HI MArtin, I am using here the infiniband having speed more than 10 gbps..Can you suggest some option to scale better in this case. What % imbalance is being reported in the log file? What fraction of the load is being

[gmx-users] questions in Running MDS over docked poses

Hi There, I am running MDS over the docked poses to check the stability of the docked poses using gromacs. I have few doubts about selecting parameters for the same, If anybody have tried such thing earlier, please suggest me for the same. Should I keep pressure coupling over the simulation ? For

[gmx-users] replicating a view in pymol for multiple files

Hi There, My apologies to ask a question not related to gromacs here. I want to know how can I generate a particular view in PYMOL ? like if I am having around 50 pdb files and I want to visualize them all in a particular view (giving differetnt color to different residue,,etc) Can I do it by

Re: [gmx-users] questions in Running MDS over docked poses

. With Thanks, Vivek 2008/11/10 Justin A. Lemkul [EMAIL PROTECTED] vivek sharma wrote: Hi There, I am running MDS over the docked poses to check the stability of the docked poses using gromacs. I have few doubts about selecting parameters for the same, If anybody have tried such thing

[gmx-users] Running MDS over docked poses

Hi There, I am trying to run MDS over some docked result generated by Autodock4, but I am not sure of the forcefield I should use. If anybody have tried doing it before, please guide me for the same. For generating topology of ligand, I am using PRODRG server, which has limited option for

Re: [gmx-users] Running MDS over docked poses

grompp with -n yourindexfile.ndx Note sure, if this is makes physically sense though. Andreas From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of vivek sharma Sent: 07 November 2008 09:00 To: Discussion list for GROMACS users Subject: [gmx-users] Running MDS over docked poses

Re: [gmx-users] how much ns

Hi Marc, Can you give an approximate time estimate for too short and too long time of simulation, if I am running simulation for protein in water to see the conformational changes ? With Thanks, Vivek 2008/11/6 Marc F. Lensink [EMAIL PROTECTED] On Thu, Nov 06, 2008 at 03:08:53PM +0530, Bhawana

Re: [gmx-users] Running MD only for selected part of molecule

to be done than that (like during genpr option). Please explainAs I have no idea to play with such option... My apologies again, if these small question irritates you... With Thanks, Vivek 2008/10/15 Justin A. Lemkul [EMAIL PROTECTED] vivek sharma wrote: Dear Justin, Thanks for your

[gmx-users] ErrorBox was shifted at least 10 times. Please see log-file

Hi Tehre, i am running a job by keeping a part of molecule freeze by using the .mdp option __ energygrps_excl= Terminal Terminal Terminal SOL ! To remove computation of nonbonding interactions between the frozen groups with each other and surroundings (i.e.

Re: [gmx-users] ErrorBox was shifted at least 10 times. Please see log-file

K. gen_vel = yes gen_temp= 300.0 gen_seed= 173529 ; Non-equilibrium MD stuff freezegrps = freeze freezedim= Y Y Y With Thanks, Vivek 2008/10/17 Justin A. Lemkul [EMAIL PROTECTED] vivek sharma wrote: Hi Tehre, i am

Re: [gmx-users] Running MD only for selected part of molecule

Dear Justin, Thanks for your reply.. But I am not getting how and where should I give the option of energy_excl. For freezing a part of molecule ? what are the other checks to be done for the same ? With Thanks, Vivek 2008/10/14 Justin A. Lemkul [EMAIL PROTECTED] vivek sharma wrote: 2008

[gmx-users] g_lie + running MDS for a ligand only

Hi All, I want to use g_lie function of gromacs to calculate the binding free energy og a ligand with the protein. For the same I need to run two MDS, one for ligand only and one for ligand+protein complex (please correct if I am wrong). What are the checks that I should take care in this case,

Re: [gmx-users] Unable to view trajectory in pymol or vmd

Hi David, Thanks for your response. I was not loading any pdb file. Do I need to do so ? where ? With Thanks, Vivek 2008/10/14 David van der Spoel [EMAIL PROTECTED] vivek sharma wrote: Hi There, I have few MD trajectory, I want to analyze them visually (other than ngmx option as it gives

Re: [gmx-users] Running MD only for selected part of molecule

Hi there, I tried the mdrun by keeping a group of residue position restrained, and it is working well (verified by comparing RMSD plot for the same), thanks for your suggestions regarding the same. But, I have seen that the part of the molecule I kept for PR is still having some motion, how can I

Re: [gmx-users] Running MD only for selected part of molecule

2008/10/14 Justin A. Lemkul [EMAIL PROTECTED] vivek sharma wrote: Hi there, I tried the mdrun by keeping a group of residue position restrained, and it is working well (verified by comparing RMSD plot for the same), thanks for your suggestions regarding the same. But, I have seen

[gmx-users] Unable to view trajectory in pymol or vmd

Hi There, I have few MD trajectory, I want to analyze them visually (other than ngmx option as it gives very few option). I tried for opening those trajectories in vmd and pymol but not able to view them. It shows me the trajectory loaded, but not viewing anything. Is there any check to be doen

Re: [gmx-users] Running MD only for selected part of molecule

or parts of the molecule you choose. As a bonus, you will not spend resources computing intramolecular interactions in the rigidified regions. Sam On Oct 10, 2008, at 6:10 AM, Justin A. Lemkul wrote: vivek sharma wrote: Hi justin, My apologies for asking you so many small queries. Can

Re: [gmx-users] Running MD only for selected part of molecule

restraining ?? With Thanks, Vivek 2008/10/10 Justin A. Lemkul [EMAIL PROTECTED] vivek sharma wrote: Hi there, I want to run MD over a part of my molecule , for few residues only (not the whole molecule). Can I do it using GROMACS ? I searched for the online documentation and mailing list

[gmx-users] Converting 2-d molecule to 3-D

Hi there, Is there any open source package to convert 2-D structure of a molecule to 3-D structure ? If anybody have tried such thing, please suggest me te way to do the same. I am having openbabel on my system, does openbabel i shaving such functionality ? please suggest ? With thanks,

Re: [gmx-users] Running MD only for selected part of molecule

wrote: vivek sharma wrote: Thanks Justin, My goal is to keep certain part fixed and move only a few of the residues (case is like providing flexibility to the site of interest only). SO , do I need to specify the residue using some index file ? or is there some other way to specify the part

Re: [gmx-users] Running MD only for selected part of molecule

Hi justin, My apologies for asking you so many small queries. Can you suggest any good tutorial or reference that talks about this issue of running MD over a selected part of molecule. With Thanks, Vivek 2008/10/10 vivek sharma [EMAIL PROTECTED] hI justin, Thanks for your response. do I

[gmx-users] Running MD only for selected part of molecule

Hi there, I want to run MD over a part of my molecule , for few residues only (not the whole molecule). Can I do it using GROMACS ? I searched for the online documentation and mailing list, but unable to get appropriate information. If somebody has already tried such things earlier, please

[gmx-users] Continuing a crashed run when running simulation in parts

Hi There, I am running a long MDS for one protein molecule in water, To avoid error I am running the simulation in parts like 20 nsec each. Each time I am creating a new tpr, trr and edr using the tpbconv and mdrun. Last time when I fired a job for 60-80 nsec then the job crashed because of some

Re: [gmx-users] setting constraints to incomplete protein structures

Hi yeo, I have one query related to the MD you are trying. What I understood here is you are trying different conformation of your protein molecule for docking it with ligand (please, correct me if I am wrong) I am also trying the same, But not finding any criteria to pick up the conformation of

Re: [gmx-users] Finding centroid for a bunch of residues

Hi all experts, Can I select all the residue which are lying within a given distance from one residue ?, using any of the tool in pymol, vmd, chimera or gromacs. Whether the option of g_hbond which gives the pair within a particular distance can be used for the same purpose ?, FYI, I am having

Re: [gmx-users] setting constraints to incomplete protein structures

Hi Yeo, Actually, I tried the same thing to get various conformation for the protein I am dealing with. For sampling the frames (i.e. conformation ) I tried two approaches... first I have taken frames which are at equal distance on trajectory without looking for any parameter ( randomly). Second

[gmx-users] Finding centroid for a bunch of residues

Hi there, This is the question out of gromacs..but I need it urgently.. and I hope this is the only place where I can get such expert to solve my query... while trying to restrict my MDRUN for a particular site of the protein molecule I want to visualize the site and find out the centroid for the

[gmx-users] Re: Finding centroid for a bunch of residues

Hi Everybody, adding a little to my question, can I view the co-ordinate of an atom by pointing at it using mouse or can I select an atom by specifying its co-ordinate only..? Does any of the tool in chimera, pymol, vmd is having such facility.? 2008/10/6 vivek sharma [EMAIL PROTECTED] Hi

Re: [gmx-users] Re: Finding centroid for a bunch of residues

..? Does any of the tool in chimera, pymol, vmd is having such facility.? 2008/10/6 vivek sharma [EMAIL PROTECTED] Hi there, This is the question out of gromacs..but I need it urgently.. and I hope this is the only place where I can get such expert to solve my query... while

[gmx-users] different g_hbond result for two run

hi all, I was trying to analyze some h_bond interaction for a protein with one ligand. I tried two runs for the same one for 5 nsec and another for 10 nsec. What I found here is that, the h-bonds present in the 5 nsec trajectory are more than that in 10 nsec trajectory, h-bonds in 10 nsec run

[gmx-users] superimposing molecules

hi All, My apologies for putting a question out of gromacs. I was trying to superimpose pdb entry of one molecule over other, I tried it using PYMOL, CHIMERA and vmd ..they are simply opening one molecule over other. Is there any specific function in any of the visualization tool, that can solve

[gmx-users] Docking using MDS

Hi There, I am trying to run MD simulation for screening my docking result, but I am not aware of what are the parameters and analysis we can do for docking by using MD simulation. If anybody have tried the similiar things using GROMACS, Please help me in this regard. With Thanks, VIvek

Re: Fwd: [gmx-users] Performance problems with more than one node

Hi Carsten and Justin, I am interrupting here as I tried with the option u suggested.. I tried cut-off instead of PME as coulombtype option it is running well for 24 processor, then I tried with 60 processor , following is the result I am getting Result1: When tried for 50 ps of run on 24

[gmx-users] Too many LINCS warning

Hi There, I am trying to scale my system(system with 45000 atoms which is one protein molecule in water box) to run on more number of processor I have asked a number of related queries, but now I am getting warning pasted below... Fatal error: Too many LINCS warnings (11587) - aborting to avoid

Re: [gmx-users] Too many LINCS warning

[EMAIL PROTECTED] vivek sharma wrote: Hi There, I am trying to scale my system(system with 45000 atoms which is one protein molecule in water box) to run on more number of processor I have asked a number of related queries, but now I am getting warning pasted below... Fatal error: Too

Re: [gmx-users] Performance problems with more than one node

Hi friends, I am also facing the similar problem when tried to scale gromacs for more number of processors , I have tried one job using gromacs on EKA, in an attempt to scale it for more number of processor I am able to get the reduction in simulation time upto 20 processors, it is taking more

Re: [gmx-users] Performance problems with more than one node

Sorry for the incomplete mail...i sent it by mistake what i want to add is I am not able to run it with any of the option.any help and suggestion will be highly appreciated. FYI size of my system is around 45000 atoms. Thanks in advance, Vivek 2008/9/25 vivek sharma [EMAIL PROTECTED] Hi

[gmx-users] Error in .gro after energy minimization

Hi there, while running energy minimization using the steep integrator.. I am getting corrupted .gro file ...which is having irregularity in file format.. Can anybody help me in figuring out the reason and how can I get rid of this problem ? I am not able to continue for further steps with this

[gmx-users] using vmd output for MDRUN

Hi There, Following is the scenario I am trying for MDS I am using vmd to modify the position of my molecule, and then output from vmd is in .pdb format. for .top file I have generated those files from pdb2gmx and edited them manually as suggested in drug-enzyme tutorial by J E Kerrigan. Now, I

[gmx-users] sampling conformation on the basis of RMSD value

Hi There, I have a 5 nsec trajectory file for my system...and a RMSD plot for the same. while doing simulation I have sampled the frame at each 500 ps, Now I want to choose conformation on the basis of RMSD values, like conformation which has RMSD difference of some value say A nanometer. Can

Re: [gmx-users] Gromacs parellal run:: getting difference in two trajectories

: Terminating job Is this information is helpfull in figuring out the problem. Please, advice With Thanks, Vivek 2008/9/11 Carsten Kutzner [EMAIL PROTECTED] vivek sharma wrote: Hi There, I am running gromacs parellal version

Re: [gmx-users] Gromacs parellal run:: getting difference in two trajectories

Sorry, I forgot to mention that one cofactor NDP, I added in my molecule using PRODRG server. 2008/9/12 vivek sharma [EMAIL PROTECTED] Hi Carsten, Thanks for your reply. Actually I am running MD simulation on a protein molecule with 270 residues(2687 atoms), after adding water it is having

Re: [gmx-users] Gromacs parellal run:: getting difference in two trajectories

grid, which has to be communicated among the processors. PME order 4 will be better suited for such a high parallelization, but in general for Gromacs 3.x you should have at least a few thousand atoms per processor, less than 1000 won't give you decent scaling at all. Carsten vivek sharma

[gmx-users] Gromacs parellal run:: getting difference in two trajectories

Hi There, I am running gromacs parellal version on cluster, with different -np options. On analyzing the 5 nsec trajectory using ngmx, I am finding difference in the trajectory of two similar runs (only thing varying in two runs in -np i.e 20 and 64 ), where mdp file and input files are same in

Re: [gmx-users] Gromacs parellal run:: getting difference in two trajectories

/11 David van der Spoel [EMAIL PROTECTED] vivek sharma wrote: Hi There, I am running gromacs parellal version on cluster, with different -np options. On analyzing the 5 nsec trajectory using ngmx, I am finding difference in the trajectory of two similar runs (only thing varying in two runs

Re: [gmx-users] Using gromacs for docking purpose

? With Thanks, Vivek 2008/9/10 Justin A. Lemkul [EMAIL PROTECTED] vivek sharma wrote: Hi Everybody, I am running MD simulation for getting various conformation of a molecule, that can act as better receptor for docking purpose. While doing so, I got a number of doubts. Firstly what should

[gmx-users] Doubt in Energy minimization and Position restrained

Hi there, My apologies for asking question from basics. I have one doubt regarding order of Position restrained and Energy minimization. While running Position restrained, it soaks water molecule well within the protein molecule. In doing so on rearranging atoms it will again raise the energy of

[gmx-users] Forcefield to choose

Hi everybody, I am running MDS for protein molecule using GROMACS, but I am not sure of which forcefield I should use. Can anybody suggest me the criteria for choosing forcefield ? Also, I am using drug-enzyme tutorial by John E. Kerrigan titled GROMACS Tutorial for Drug – Enzyme Complex. where

[gmx-users] Using .pdb only

Hi There, I am usinng gromacs for running MDS of one protein, Can I use the pdb file only without generating the .gro file i.e. without using pdb2gmx ? If no, then how can I avoid addition of hydrogen during pdb2gmx ? With Thanks, Vivek ___ gmx-users

[gmx-users] Warnings while grompp_d

Hi there, while running gromacs in parallel with double precision, during grompp_d I am getting following warning in output file along with other status.. ... ... ... WARNING 1 [file 1XU9_A.top, line unknown]: The largest charge group contains 12 atoms. Since atoms only see each other when

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

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. How should I use the g_energy command or which .edr file I should use? Any suggestion would be of great help.. With Thanks, Vivek

[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

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

? With Thanks, Vivek 2008/8/27 Jochen Hub [EMAIL PROTECTED] 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

[gmx-users] Error while running gromacs in parellel

Hi There, I am running gromacs in parellel using mpirun (using submit option). While doing so output file gave me error as follow srun: error: n826: task32: Terminated srun: Terminating job srun: error: n827: task40: Segmentation fault I am running gromacs for the first time (in parellel).

[gmx-users] HELP::Running Gromacs in parellel

Hi There, I am running gromacs on parellel system using the submit command. Commands are running fine, but the .trr file I got is not matching with the trr file I got while running command in serial. Also, I am getting a number of log files(equal to number of nodes I am choosing). How should I

[gmx-users] Visualizing gromacs result

Hi, Can anybody tell which visualization tool is better out of vmd/pymol/gopenmol to visualize gromacs result.? Thanks in advance, Vivek ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search

[gmx-users] MDRUN with MPIRUN

Hi There, I am trying to run the gromacs with mpirun, but don't know the exact commands for running gromacs with mpirun. If, somebody can give the exact command to run mdrun with MPI. It will be of great help for me to do my job. Thanks in advance, Vivek

Re: [gmx-users] MDRUN with MPIRUN

] [mailto:[EMAIL PROTECTED] On Behalf Of vivek sharma Sent: 20 August 2008 12:44 To: Discussion list for GROMACS users Subject: [gmx-users] MDRUN with MPIRUN Hi There, I am trying to run the gromacs with mpirun, but don't know the exact commands for running gromacs with mpirun. If, somebody

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