[gmx-users] (no subject)

Dear All I am learning molecular simulation using Gromacs. when I complete my simulation, How can I check that my simulation run was o.k. and the output so obtained can be trusted. Is there any easy calculation, which could be performed. Thanks in advance. msnayeem -- gmx-users mailing list

RE: [gmx-users] Problem with tabulated potentials for 3 different atoms

Hi, I don't want to get into discussions on drugs and I don't know if you already switched package, but I'l post my answer anyhow. The energy groups in each pair on your energygrp_table line should be separated by a space. The table files should contain all columns, unused columns are allowed

Re: [gmx-users] (no subject)

On 20/04/2010 4:39 PM, shahid nayeem wrote: Dear All I am learning molecular simulation using Gromacs. when I complete my simulation, How can I check that my simulation run was o.k. and the output so obtained can be trusted. Is there any easy calculation, which could be performed. No. These

Re: [gmx-users] CG-MD simulation of protein, always crash with protein

The representation of extended regions (b-sheets) is more stable using elastic bonds than a dihedral angle because the flexibility of the force field makes possible the occurrence of situations where the two bonds get aligned and therefore the plan used to defined the dihedral can not be

Re: [gmx-users] about H-Bonds g_hbond

Hi, Please submit a bugzilla, assign it to me, and I'll try to fix it along with heaps of other things. Erik Marklund Justin A. Lemkul skrev: babu gokul wrote: Hi all I am getting an error in g_hbond such as Program g_hbond_d, VERSION 4.0.7 Source code file: gmx_hbond.c, line: 565

Re: [gmx-users] (no subject)

Mark Abraham skrev: On 20/04/2010 4:39 PM, shahid nayeem wrote: Dear All I am learning molecular simulation using Gromacs. when I complete my simulation, How can I check that my simulation run was o.k. and the output so obtained can be trusted. Is there any easy calculation, which could be

Re: [gmx-users] Force output

I think this one can help you: http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000306 You can download a code that gives you the forces from the following website: http://projects.eml.org/mbm/website/fda_gromacs.htm Ilona Quoting Avisek Das avi...@stanford.edu: Dear

[gmx-users] Problem with tabulated potentials for 3 different atoms

Berk: Thanks for the help, and thanks too to the other members of the list who helped me. My simulation is working now with some energy problems, but this is another problem not related to the software. The missing space characters were a typing mistake. About drugs and other subjets of your

RE: [gmx-users] Problem with tabulated potentials for 3 different atoms

From: mrvartore...@gmail.com Date: Tue, 20 Apr 2010 06:33:09 -0300 To: gmx-users@gromacs.org Subject: [gmx-users] Problem with tabulated potentials for 3 different atoms Berk: Thanks for the help, and thanks too to the other members of the list who helped me. My simulation is working

Re: [gmx-users] about H-Bonds g_hbond

Erik Marklund wrote: Hi, Please submit a bugzilla, assign it to me, and I'll try to fix it along with heaps of other things. This bug has been outstanding for some time already: http://bugzilla.gromacs.org/show_bug.cgi?id=334 -Justin Erik Marklund Justin A. Lemkul skrev: babu

[gmx-users] genbox

Hello, I want to use a file.pdb which has 8 chain of polypeptide, each chain contains 6 residues. I need to expand it to 12 chains of 6 rsidues so I need to add 4 chains or in the other word 24 residues. I think I have to use genbox, so I make another copy of file.pdb and rename it to

Re: [gmx-users] genbox

fahimeh bafti wrote: Hello, I want to use a file.pdb which has 8 chain of polypeptide, each chain contains 6 residues. I need to expand it to 12 chains of 6 rsidues so I need to add 4 chains or in the other word 24 residues. I think I have to use genbox, so I make another copy of file.pdb

Re: [gmx-users] Compiling Gromacs 4.0.7 on AIX 5.3

Hello again I followed your advices this time here's what I did : downloading gromacs 4.0.7 downloading fftw 2.1.5 initializing environment variables (modified to fit my configuration (pwr5) : export LDFLAGS='-L/usr/local/lib' export CPPFLAGS='-I/usr/local/include' export

Re: [gmx-users] Compiling Gromacs 4.0.7 on AIX 5.3

I've never worked with such architecture, but I do remember seeing a few posts in the past, some of which may be useful. Perhaps this one will hold some clues: http://lists.gromacs.org/pipermail/gmx-users/2007-April/027074.html Sorry I can't provide much more than this, but I thought I'd at

[gmx-users] Problems with g_energy

Hi folks I have recently encountered some problems with g_energy which I have not encountered before. I am running simulations for 32 molecular cages on 16 cpus in our local cluster. The maximum time for any one job is 24 hrs. Therfore after 24 hrs the jobs are killed so I countinue the job using

RE: [gmx-users] genbox

Thank you Justin but I end up with a new error. now in the insert.pdp file I have a molecule which I need to add 4 copy of that inside the solute.pdb genbox_d -ci insert.pdb -nmol 4 -cp solute.pdb but it gave me: Fatal error: more then one residue in insert molecules program terminated

Re: [gmx-users] about H-Bonds g_hbond

Justin A. Lemkul skrev: Erik Marklund wrote: Hi, Please submit a bugzilla, assign it to me, and I'll try to fix it along with heaps of other things. This bug has been outstanding for some time already: http://bugzilla.gromacs.org/show_bug.cgi?id=334 -Justin Ok. Thanks. I guess I was

Re: [gmx-users] Problems with g_energy

Gavin Melaugh wrote: Hi folks I have recently encountered some problems with g_energy which I have not encountered before. I am running simulations for 32 molecular cages on 16 cpus in our local cluster. The maximum time for any one job is 24 hrs. Therfore after 24 hrs the jobs are killed so

Re: [gmx-users] genbox

fahimeh bafti wrote: Thank you Justin but I end up with a new error. now in the insert.pdp file I have a molecule which I need to add 4 copy of that inside the solute.pdb genbox_d -ci insert.pdb -nmol 4 -cp solute.pdb but it gave me: Fatal error: more then one residue in insert molecules

[gmx-users] Finishing time donot showing

Hello all i got a system crash at some steps.. after creating the new .trr file using command tpbconv and running MDS by mdrun command the approximate finishing time is not showing. and also a warning is showing as WARNING: this run may generate approximately 4583292 Mb of data

Re: [gmx-users] Finishing time donot showing

On Apr 20, 2010, at 9:14 AM, Bharath.K wrote: Hello all i got a system crash at some steps.. after creating the new .trr file using command tpbconv trr file with tpbconv? you mean tpr? and running MDS what is MDS? by mdrun command the approximate finishing time is not showing. and

Re: [gmx-users] Finishing time donot showing

Bharath.K wrote: Hello all i got a system crash at some steps.. after creating the new .trr file using command tpbconv and running MDS by mdrun command the approximate finishing time is not showing. and also a warning is showing as WARNING: this run may generate approximately

Re: [gmx-users] Problems with g_energy

Hi justin Basically the gmxdump produces the same as below as does gmxcheck. gmxcheck also produces the following: Checking energy file ener.edr Opened ener.edr as single precision energy file frame: 0 (index 0), t: 0.000 Reading energy frame 4000 time 4.000

Re: [gmx-users] Problems with g_energy

Gavin Melaugh wrote: Hi justin Basically the gmxdump produces the same as below as does gmxcheck. gmxcheck also produces the following: Checking energy file ener.edr Opened ener.edr as single precision energy file frame: 0 (index 0), t: 0.000 Reading energy frame

Re: [gmx-users] Problems with g_energy

Cheers Justin Just to make sure then to run the simulation with -maxh to avoid the 24hr cut off I use the command: mdrun -pd -s topol.tpr -maxh 23 (using 23 hrs to be overcautious) then to restart: mdrun -pd -cpi state.cpt Do I have to use the -append option in the above command to continue

[gmx-users] parallel simulation in dual core PC

Hi, I want to use my dual core PC to do the simulation. The version of GROMACS installed is version 4.0.5. According the message post by others on mailing list before. I type lamboot first, and type the commend: mpirun -np 2 mdrun_mpi -s 200ns.tpr -e 200ns.edr -o 200ns.trr -g 200ns.log -c

Re: [gmx-users] Problems with g_energy

Gavin Melaugh wrote: Cheers Justin Just to make sure then to run the simulation with -maxh to avoid the 24hr cut off I use the command: mdrun -pd -s topol.tpr -maxh 23 (using 23 hrs to be overcautious) then to restart: mdrun -pd -cpi state.cpt Do I have to use the -append option in the

RE: [gmx-users] genbox

Thanks :) but I couldn't manage with that, it makes the same error with editconf as well, the problem was related to having more than one residue inside insert.gro I did it at the end with genconf genconf -nbox 2 2 2 (as u want) -f file.gro -o file_replicate.pdb it will simply replicate

[gmx-users] Size of generating data

hi all I'm running simulation for a protein of about 150 amino acids for 100 steps i.e 2 ns in a system of about 35 GB disk space. is there any way to know the approximate size of generating data. -- Bharath.K.Chakravarthi Ph:9535629260 -- gmx-users mailing list

Re: [gmx-users] Finishing time donot showing

Sorry MDS means MD simulation the commands are as follows tpbconv -s md.tpr -f md_traj.chk.trr -o md_01.tpr -until 1000 this shows last step before crashing and starts from there until 1000 then mdrun -s md_01.tpr -o md_traj_01.trr -c minim_water.gro -g md.log -e minim_ener_01.edr On Tue, Apr

Re: [gmx-users] Size of generating data

On Tuesday 20 April 2010 18:02:50 Bharath.K. Chakravarthi wrote: hi all I'm running simulation for a protein of about 150 amino acids for 100 steps i.e 2 ns in a system of about 35 GB disk space. is there any way to know the approximate size of generating data. The grompp

[gmx-users] interaction parameter, polyolefin solution, ternary system

Hello, My research is concerned with computational thermodynamics of compressible polyolefin solution (polyethylene in n-Hexane as solvent). I am interested in calculation of interaction parameter of ternary system of polyethylene/n-Hexane/ ethylene. Ethylene is unreacted monomer in the solution.

Re: [gmx-users] Finishing time donot showing

tpbconv -s md.tpr -f md_traj.chk.trr -o md_01.tpr -until 1000 this shows last step before crashing and starts from there until 1000 then mdrun -s md_01.tpr -o md_traj_01.trr -c minim_water.gro -g md.log - e minim_ener_01.edr Nothing seem particularly wrong! May be you write your

Re: [gmx-users] genbox

fahimeh bafti wrote: Thanks :) but I couldn't manage with that, it makes the same error with editconf as well, the problem was related to having more than one residue inside insert.gro editconf should not have a problem placing multi-residue molecules within a box. That is its main

Re: [gmx-users] Finishing time donot showing

XAvier Periole wrote: tpbconv -s md.tpr -f md_traj.chk.trr -o md_01.tpr -until 1000 this shows last step before crashing and starts from there until 1000 then mdrun -s md_01.tpr -o md_traj_01.trr -c minim_water.gro -g md.log -e minim_ener_01.edr Nothing seem particularly wrong! May

Re: [gmx-users] Finishing time donot showing

I'm using gromacs-3.3.3 and here is the parameter .. .. nstxout = 500 nstvout = 1000 nstfout = 0 nstlist = 100 nstlog = 100 nstenergy = 10 nstxtcout = 500 .. .. for writing trajectories in .mdp file and

Re: [gmx-users] Finishing time donot showing

Bharath.K wrote: I'm using gromacs-3.3.3 and here is the parameter .. .. nstxout = 500 nstvout = 1000 nstfout = 0 nstlist = 100 nstlog = 100 nstenergy = 10 nstxtcout = 500 .. .. for writing trajectories

Re: [gmx-users] Finishing time donot showing

no i did not used -v flag at that command may be thats the mistake thank u Justin On Tue, Apr 20, 2010 at 10:54 PM, Justin A. Lemkul jalem...@vt.edu wrote: Bharath.K wrote: I'm using gromacs-3.3.3 and here is the parameter .. .. nstxout = 500 nstvout = 1000

[gmx-users] Tabulated potentials

Hi Gromacs users, previously I've posted my situation with a simulation and I'm still confused: I have 3 groups of different atoms: A, B and C, and tabulated bonding and non-bonding potentials. The tabulated bonded potentials are specified in the files: table_b1.xvg table_a1.xvg table_a2.xvg

Re: [gmx-users] Finishing time donot showing

On Apr 20, 2010, at 7:39 PM, Bharath.K. Chakravarthi wrote: no i did not used -v flag at that command may be thats the mistake thank u Justin On Tue, Apr 20, 2010 at 10:54 PM, Justin A. Lemkul jalem...@vt.edu wrote: Bharath.K wrote: I'm using gromacs-3.3.3 and here is the parameter ..

Re: [gmx-users] Finishing time donot showing

and XAvier [?] On Tue, Apr 20, 2010 at 11:09 PM, Bharath.K. Chakravarthi bharath.chakravar...@gmail.com wrote: no i did not used -v flag at that command may be thats the mistake thank u Justin On Tue, Apr 20, 2010 at 10:54 PM, Justin A. Lemkul jalem...@vt.eduwrote: Bharath.K wrote:

Re: [gmx-users] Finishing time donot showing

that means generating a trajectory file for every 10 steps rite then i may need more disk space On Tue, Apr 20, 2010 at 11:41 PM, XAvier Periole x.peri...@rug.nl wrote: On Apr 20, 2010, at 7:39 PM, Bharath.K. Chakravarthi wrote: no i did not used -v flag at that command may be thats the

Re: [gmx-users] Tabulated potentials

Hi I think this is what you need to do: (1) Ensure that the topol.top and index.ndx files are set up in the manner described on the wikki. (2) Put in the mdp file the following: energygrps = A B C energygrp_table = A C B B B C (3) Now create a set of files as follows table.xvg -

Re: [gmx-users] Finishing time donot showing

Bharath.K. Chakravarthi wrote: that means generating a trajectory file for every 10 steps rite then i may need more disk space The nstlist parameter has nothing to do with trajectory output. It is the frequency with which the neighborlist is updated. Setting this value too high can

Re: [gmx-users] Finishing time donot showing

Hi Bharath, It means updating the neighbor lists every 10 steps. You might want to check the manual on those options. Also, you're writing full precision coordinates and velocities very often, and you're writing coordinates to the .xtc file as often as to the .trr file, which is redundant anyhow.

[gmx-users] High quality movies, bmp frames and videomach=poor quality

Hi, I am using tachyon to get high quality still pictures by generating a .dat file, changing the render numbers and then typing this command in the window N:/myhome/VMD1.8.7/tachyon_WIN32.exe -aasamples 12 plot01.dat -format -o plot01.tga This gives great images but now I am stuck on

Re: [gmx-users] High quality movies, bmp frames and videomach=poor quality

mencoder is pretty good but I do not guaranty the size! mencoder mf://file-.tga -mf fps=16:type=tga -ovc lavc -lavcopts vcodec=mjpeg -oac copy -o movie.avi On Apr 20, 2010, at 8:36 PM, Jennifer Williams wrote: Hi, I am using tachyon to get high quality still pictures by generating

[gmx-users] 'SHAKE' : gromacs 4.0.7

Hello gromacs users: I installed the new version of gromacs and tried to run 'mdrun_mpi' in parrallel but it gives the error pasted below. When i switched the constrain from 'shake' to 'lincs' it runs. I know 'shake' algorithm compilation was done but i don't why i am getting this

Re: [gmx-users] 'SHAKE' : gromacs 4.0.7

Ramachandran G wrote: Hello gromacs users: I installed the new version of gromacs and tried to run 'mdrun_mpi' in parrallel but it gives the error pasted below. When i switched the constrain from 'shake' to 'lincs' it runs. I know 'shake' algorithm compilation was done but i don't

Re: [gmx-users] 'SHAKE' : gromacs 4.0.7

When you run GROMACS in parallel, by default it does domain descomposition, so if your constraints run across the charge groups, SHAKE can not run. El mar, 20-04-2010 a las 14:49 -0700, Ramachandran G escribió: Hello gromacs users: I installed the new version of gromacs and tried to run

Re: [gmx-users] parallel simulation in dual core PC

On 21/04/2010 12:55 AM, Hsin-Lin wrote: Hi, I want to use my dual core PC to do the simulation. The version of GROMACS installed is version 4.0.5. According the message post by others on mailing list before. I type lamboot first, and type the commend: mpirun -np 2 mdrun_mpi -s 200ns.tpr -e

Re: [gmx-users] interaction parameter, polyolefin solution, ternary system

On 21/04/2010 2:43 AM, Moeed wrote: Hello, My research is concerned with computational thermodynamics of compressible polyolefin solution (polyethylene in n-Hexane as solvent). I am interested in calculation of interaction parameter of ternary system of polyethylene/n-Hexane/ ethylene. Ethylene

[gmx-users] query on constraint-force pull code

Hi, I would like to use constraint force pull code to calculate the free energy of association of two peptide using the distance between center of mass of two peptides as reaction coordinate. I am planning to use gromacs 4. Here I have some queries: 1. Since I will constraint method, I