[gmx-users] Average pdb coordinates

Dear Friends To get coordinates at specific ps i used to use following command trjconv -f md.xtc -s md.tpr -o 2000.pdb -dump 2000 *I want average pdb coordinates between 0ps to 2000ps, How i can get it ?* Regards Rituraj -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.o

[gmx-users] Query regarding g_rmsf and g_hbond

Dear friends, I have some query regarding g_rmsf and g_hbond 1) Through g_rmsf we can plot rmsf Vs atom number (it is by default) but i want to plot rmsf Vs time, how i can do that? 2) Through g_hbond we can plot number of H-bonds Vs Time (By default) but i want to plot number of h-bonds Vs res

[gmx-users] Phosphorylation of protein

Dear friends, I want to add a phosphate (PO4) group to a amino acid residue (serine) in my protein molecule (phosphorylation of protein). Is is possible to do by in-silico (with help of Gromcs or by any other server)? Please help me in this. Thank you :) Rohan On Wed, May 19, 2010 at 7:32 PM,

[gmx-users] PCA tutorial

Dear friends, I want to do PCA for my MD data. If anybody know the tutorial regarding PCA, please let me know. Thanks in advanced Regard Rohan On 2/1/10, gmx-users-requ...@gromacs.org wrote: > Send gmx-users mailing list submissions to > gmx-users@gromacs.org > > To subscribe or unsubs

[gmx-users] Plot renumbering

Hello friends, As Justin replied at carla query about structure deformation after the pdb2gmx & the new number retain till end. My PDB starts at 24 to 200 aa, While running xmgrace (after complete simulation) the rmsd plot is from 1 to 176aa. I understood by previous mail that gromacs renumbered

[gmx-users] Problem in g_rms

I want get rmsd deviation between NMR structure and the simulated result, but i am getting following error in following command. g_rms -s em.tpr -f md.trr -o rsmd_Calpha.xvg WARNING: topology has 50772 atoms, whereas trajectory has 22899 --- Pro

[gmx-users] position restrained dynamics & protein size

gt; 1DPPC115 721 1.711 4.346 3.523 > 1DPPC116 722 1.861 4.344 3.549 > 1DPP C33 723 1.394 3.827 1.098 > 1DPP C34 724 1.402 3.868 1.324 > > 1DPP C35 725 1.337 3.651 1.249 > 1DPP N 726 1.324 3.795 1.223 > 1DPP C32 727 1.185 3.841 1.213 > 1DPP C31 728 1.074 3.797

[gmx-users] Re: Regarding g_rmsf

ue MET 1 not found in rtp entry with 9 atoms > > > > please help me sortout these problem. > > > > -- > > Ashish Pandey > > NIPER India > > -- > > gmx-users mailing listgmx-users@gromacs.org > > http://lists.gromacs.org/mailman/listinfo/gmx-us

[gmx-users] Re: xmgrace plot

> -- > > gmx-users mailing listgmx-users@gromacs.org > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at http://www.gromacs.org/search before > posting! > > Please don't post (un)subscribe requests to the list. Use the

[gmx-users] RMSD Vs Residue no by Grace

Dear friends, I am able to plot, RMSD between Time (ps) by following command by using GRACE.. g_rms -s md.tpr -f md.xtc xmgrace rmsd.xvg How we can I plot a graph betwwen RMSD and residue no ..?? My aim is to find RMSD at each residues. How i can do that? looking forward for u r important sugg

[gmx-users] How to select Force field

] How to neutralize net charge of protein and > why > To: Discussion list for GROMACS users > Message-ID: <4a994e0a.90...@vt.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > > Please do not include the text of the digest when composing a m

[gmx-users] How to neutralize net charge of protein and why

gt; > > > > > > > > _______ > > > gmx-users mailing listgmx-users@gromacs.org > > > http://lists.gromacs.org/mailman/listinfo/gmx-users > >

[gmx-users] DSSP problem

acing the PRODRG charges (Lucio Ricardo Montero Valenzuela) >4. Re: Replacing the PRODRG charges (Mark Abraham) >5. how to include ionic strength (amri ta) >6. Re: how to include ionic strengt

[gmx-users] DSSP problem

Dear all I want ti install DSSP for visualization of secondary structure in gromacs analysis. I am doing following procedure.. Copy the executable "dsspcmbi" to /usr/bin or /usr/local/bin ln -s dsspcmbi dssp And running it for my Pdb like that dssp file.pdb file.dssp BUt I am getting error

[gmx-users] Gromacs output analysis

Hello to everybody I need the gromacs analysis document. I mean i want to do analysis (like; RMSD, traj)of my result which I got after simulation of protein molecule. If anybody having any PDF or web link emphasis the analysis part, please forword me... Thank you Rituraj On Wed, Jun 3, 2009 at 9:

[gmx-users] Problem in fianl step of MD

Hi .. I am using gromacs 4.0 for simulating a protein molecule. i am getting following problem during md run[md.mdp dt =0.002 ; ps ! nsteps = 10 ; total 200.0 ps ] t = 47.530 ps: Water molecule starting at atom 46763 can not be settled. Check for bad contacts and/or reduce the timestep.