Re: [gmx-users] genion doubt

HI I'm not sure about this kind of error but as per my knowledge the problem might be with the parameter cpp in mdp file. In my mdp file it is as follows title = ecoli_nusG cpp = /usr/bin/cpp define = -DPOSRES constraints = all-bonds integrator = md dt = 0.001 ; ps ! nsteps = 10 ; total

Re: [gmx-users] rmsd between different monomers

you said you have used online server for superimposition ... which one you used... try TOPMATCH server On Sun, May 9, 2010 at 5:31 PM, Anupam Nath Jha anu...@mbu.iisc.ernet.inwrote: Ok. But when I run this command g_rms -s setp_0.pdb -f setp_0.pdb -n ca_ind.ndx -o out it ask me

[gmx-users] To calculate surface area of of simulated protein

Hello gmx users.. Can anybody tell me is there any possibility to calculate the surface area of the protein before and after the simulation. waiting for u'r reply.. -- Bharath.K.Chakravarthi Ph:9535629260 -- gmx-users mailing listgmx-users@gromacs.org

[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] 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

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

[gmx-users] is it any serious error

hello all... when ever i run simulation i'm getting this kind of out put saying there is one warning as shown below Walking down the molecule graph to make shake-blocks initialising group options... processing index file... Analysing residue names: Opening library file

[gmx-users] simulating the effect of Ph

hello all... i know simulating the effect of temperature and pressure on the protein is there any way to study the effect of Ph on the system -- Bharath.K.Chakravarthi Ph:9535629260 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users

[gmx-users] *.xtc file is not getting created by mdrun program :(

hi there i tried to run MD and i wanted to use *.xtc file in vmd to visualize the protein but unfortunately there is no such file i given the command like this mdrun -nice 0 -v -s input3.tpr -o md_traj.trr -x md_traj.xtc -c md_final.gro -e md_ener.edr as procedure this should create md_traj.xtc

Re: [gmx-users] *.xtc file is not getting created by mdrun program :(

On Wed, Apr 14, 2010 at 5:31 AM, Bharath.K. Chakravarthi bharath.chakravar...@gmail.com wrote: Thank you for your kind replay sir sir in my .mdp file there is nstxtout instead of nstxtcout sir and it is set to 500 is this what u told... i have also attached the .mdp file in this mail

Re: [gmx-users] *.xtc file is not getting created by mdrun program :(

Thank you for your kind replay sir sir in my .mdp file there is nstxtout instead of nstxtcout sir and it is set to 500 is this what u told... i have also attached the .mdp file in this mail sir On Wed, Apr 14, 2010 at 5:18 AM, Justin A. Lemkul jalem...@vt.edu wrote: Bharath.K

Re: [gmx-users] *.xtc file is not getting created by mdrun program :(

sir should i set dat to 0 or what to do On Wed, Apr 14, 2010 at 5:32 AM, Bharath.K. Chakravarthi bharath.chakravar...@gmail.com wrote: On Wed, Apr 14, 2010 at 5:31 AM, Bharath.K. Chakravarthi bharath.chakravar...@gmail.com wrote: Thank you for your kind replay sir sir in my

Re: [gmx-users] *.xtc file is not getting created by mdrun program :(

Thank you very much for your replay sir... On Wed, Apr 14, 2010 at 5:36 AM, Justin A. Lemkul jalem...@vt.edu wrote: Bharath.K. Chakravarthi wrote: sir should i set dat to 0 or what to do I clearly stated that you should set nstxtcout 0 in my first message. Leaving any output

[gmx-users] nstfout parameter

hi .. in my *.mdp file one parameter named mstfout is set to 0 can you please tell me the use of this parameter -- Bharath.K.Chakravarthi Ph:9535629260 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at