Hi mark .. thank you for your suggestion.. My command line is g_mindist -f ..xtc -s ..tpr -od minimal.xvg -pi protein group contain information about the 284 atom (i.e. All protein atoms) .. So please suggest me the right way ..
On Thu, Mar 29, 2012 at 2:02 PM, Mark Abraham <mark.abra...@anu.edu.au>wrote: > On 29/03/2012 7:20 PM, rama david wrote: > >> Hi everybody , >> I run simulation of 4 same molecule keep apart in box >> of 4 4 4 dimension ..( 71 atom in one molecule = 71 * 4 = total atom are >> 284 ) >> force field = gromacs96 53a6 >> >> COM (center of mass) infirmation of molecules >> system size : 1.255 1.577 1.883 >> box vectors : 4.000 4.000 4.000 (nm) >> mol1 : 2.057 0.844 1.941 >> mol 2 : 2.057 0.844 3.141 >> mol 3 : 2.057 3.244 0.744 >> mol 4 : 2.057 3.244 3.141 >> >> (Four molecule are kept at the four corner of square >> of each side 2.4 nm >> four molecule are catenated in same pdb ) >> > > No they're not starting on a square. Look at those z coordinates above. > > > >> my md.mdp input is like the .. >> >> ;Neighborsearching >> ns_type = grid ; search neighboring grid cells >> nstlist = 5 ; 10 fs >> rlist = 1.0 ; short-range neighborlist cutoff (in nm) >> rcoulomb = 1.0 ; short-range electrostatic cutoff (in nm) >> rvdw = 1.0 ; short-range van der Waals cutoff (in nm) >> ; Electrostatics >> coulombtype = PME ; Particle Mesh Ewald for long-range >> electrostatics >> pme_order = 4 ; cubic interpolation >> fourierspacing = 0.16 ; grid spacing for FFT >> >> With command g_mindist , select option - 1 (Protein ) >> I got the following result.. >> >> The shortest periodic distance is 0.141718 (nm) at time 7692 (ps), >> between atoms 26 and 111 >> >> Is the simulation is behaving abnormal(I.e simulation is wrong ) or I >> have to select the option system on prompting ??? I am very new to these >> simulation field.. >> so all suggestion are appreciable ... >> > > Shrug. You've measured the inter-group distance between a group and > itself. Curiously enough, that's the length of a C-C bond, or similar. > g_mindist -h is required reading. Also, we don't even know what's in group > Protein, or your g_mindist command line. > > Mark > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before > posting! > Please don't post (un)subscribe requests to the list. Use the www > interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >
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