Hello,<br><br>Sorry I did not paste the error message part properly. Initially I am trying to study PE in vacuum (current box size 30*30*30 nm) and then I will solvate the PE with Hexane.<br><br><br clear="all">NOTE 1 [file md-July11-NPTcompression.mdp, line unknown]:<br>
The Berendsen thermostat does not generate the correct kinetic energy<br> distribution. You might want to consider using the V-rescale thermostat.<br><br>Opening library file /chem_soft/gromacs/share/gromacs/top/ffoplsaa.itp<br>
Opening library file /chem_soft/gromacs/share/gromacs/top/ffoplsaanb.itp<br>Opening library file /chem_soft/gromacs/share/gromacs/top/ffoplsaabon.itp<br>Generated 332520 of the 332520 non-bonded parameter combinations<br>
Generating 1-4 interactions: fudge = 0.5<br>Generated 332520 of the 332520 1-4 parameter combinations<br>Opening library file /chem_soft/gromacs/share/gromacs/top/spc.itp<br>Opening library file /chem_soft/gromacs/share/gromacs/top/ions.itp<br>
Excluding 3 bonded neighbours molecule type 'polymer'<br>processing coordinates...<br>double-checking input for internal consistency...<br>Velocities were taken from a Maxwell distribution at 300 K<br>renumbering atomtypes...<br>
converting bonded parameters...<br>initialising group options...<br>processing index file...<br>Opening library file /chem_soft/gromacs/share/gromacs/top/aminoacids.dat<br>Making dummy/rest group for Acceleration containing 2896 elements<br>
Making dummy/rest group for Freeze containing 2896 elements<br>Making dummy/rest group for Energy Mon. containing 2896 elements<br>Making dummy/rest group for VCM containing 2896 elements<br>Number of degrees of freedom in T-Coupling group Eth is 5373.22<br>
Number of degrees of freedom in T-Coupling group EthB is 211.89<br>Number of degrees of freedom in T-Coupling group EthE is 211.89<br>Making dummy/rest group for User1 containing 2896 elements<br>Making dummy/rest group for User2 containing 2896 elements<br>
Making dummy/rest group for XTC containing 2896 elements<br>Making dummy/rest group for Or. Res. Fit containing 2896 elements<br>Making dummy/rest group for QMMM containing 2896 elements<br>T-Coupling has 3 element(s): Eth EthB EthE<br>
Energy Mon. has 1 element(s): rest<br>Acceleration has 1 element(s): rest<br>Freeze has 1 element(s): rest<br>User1 has 1 element(s): rest<br>User2 has 1 element(s): rest<br>VCM has 1 element(s): rest<br>
XTC has 1 element(s): rest<br>Or. Res. Fit has 1 element(s): rest<br>QMMM has 1 element(s): rest<br>Checking consistency between energy and charge groups...<br>writing run input file...<br><br>
There was 1 note<br><br>There was 1 warning<br><br>-------------------------------------------------------<br>Program grompp, VERSION 4.0.7<br>Source code file: gmx_fatal.c, line: 481<br><br>Fatal error:<br>Too many warnings (1), grompp terminated.<br>
If you are sure all warnings are harmless, use the -maxwarn option.<br>-------------------------------------------------------<br><br>"My Heart is Just a Muscle In a Cavity" (F. Black)<br><br> :-) G R O M A C S (-:<br>
<br> Gromacs Runs One Microsecond At Cannonball Speeds<br><br> :-) VERSION 4.0.7 (-:<br><br><br> Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.<br> Copyright (c) 1991-2000, University of Groningen, The Netherlands.<br>
Copyright (c) 2001-2008, The GROMACS development team,<br> check out <a href="http://www.gromacs.org">http://www.gromacs.org</a> for more information.<br><br> This program is free software; you can redistribute it and/or<br>
modify it under the terms of the GNU General Public License<br> as published by the Free Software Foundation; either version 2<br> of the License, or (at your option) any later version.<br><br>
:-) grompp (double precision) (-:<br><br>processing topology...<br>turning all bonds into constraints...<br>Analysing residue names:<br>There are: 240 OTHER residues<br>There are: 0 PROTEIN residues<br>
There are: 0 DNA residues<br>Analysing Other...<br>This run will generate roughly 14 Mb of data<br><br>*********************************************************************************************************<br>
Then I altered the tc groups in mdp file to Polymer and use n option in grompp. <br><br>grompp -f md-July11-NPTcompression.mdp -c PE60_b4pr -p PE60.top -o PE60_md -n index.ndx >& output.grompp_md<br><br>(actually I wanted to what how tc group names are based on? I thought they come from residue names, then I changed index file [all] name to [polymer] <br>
index file:<br>[ special ]<br> 1 3<br>[ Polymer ]<br> 1 2 3 4<br>error:******************************************************************<br>WARNING 1 [file md-July11-NPTcompression.mdp, line unknown]:<br> Unknown or double left-hand 'rvw-switch' in parameter file<br>
<br><br>checking input for internal consistency...<br><br>NOTE 1 [file md-July11-NPTcompression.mdp, line unknown]:<br> The Berendsen thermostat does not generate the correct kinetic energy<br> distribution. You might want to consider using the V-rescale thermostat.<br>
<br>Opening library file /chem_soft/gromacs/share/gromacs/top/ffoplsaa.itp<br>Opening library file /chem_soft/gromacs/share/gromacs/top/ffoplsaanb.itp<br>Opening library file /chem_soft/gromacs/share/gromacs/top/ffoplsaabon.itp<br>
Generated 332520 of the 332520 non-bonded parameter combinations<br>Generating 1-4 interactions: fudge = 0.5<br>Generated 332520 of the 332520 1-4 parameter combinations<br>Opening library file /chem_soft/gromacs/share/gromacs/top/spc.itp<br>
Opening library file /chem_soft/gromacs/share/gromacs/top/ions.itp<br>Excluding 3 bonded neighbours molecule type 'Polymer'<br>processing coordinates...<br>double-checking input for internal consistency...<br>Velocities were taken from a Maxwell distribution at 300 K<br>
renumbering atomtypes...<br>converting bonded parameters...<br>initialising group options...<br>processing index file...<br><br>-------------------------------------------------------<br>Program grompp, VERSION 4.0.7<br>Source code file: readir.c, line: 1069<br>
<br>Fatal error:<br>358 atoms are not part of any of the T-Coupling groups<br>-------------------------------------------------------<br><br>"Rat-tat-tat Ka boom boom" (The Smashing Pumpkins)<br><br> :-) G R O M A C S (-:<br>
<br> Glycine aRginine prOline Methionine Alanine Cystine Serine<br><br> :-) VERSION 4.0.7 (-:<br><br><br> Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.<br>
Copyright (c) 1991-2000, University of Groningen, The Netherlands.<br> Copyright (c) 2001-2008, The GROMACS development team,<br> check out <a href="http://www.gromacs.org">http://www.gromacs.org</a> for more information.<br>
<br> This program is free software; you can redistribute it and/or<br> modify it under the terms of the GNU General Public License<br> as published by the Free Software Foundation; either version 2<br>
of the License, or (at your option) any later version.<br><br> :-) grompp (double precision) (-:<br><br>processing topology...<br>turning all bonds into constraints...<br>******************************************************************************************************************<br>
.<br><br>2- I have a question about doing NPT for compressing the system. Can I also do NVT for a short time and when the chain has a more realistic structure , take that structure and change the volume myself? I am just asking for the sake of learning.. This doesnt mean I am not going to do follow your advise..<br>
<br>3- Also If I want to find the pressure which gives the size I want, I need to wait till the end of simulation to see the volume (eg with g_energy) and repeat this to find the desired volume by try and error?<br><br>Thanks :)<br>
mdp file:<br><br>title = PE-Hexane <br>;define = -DPOSRES ; tells gromacs to perform position restrained dynamics/include posre.itp into topology used for position restraint<br>
pbc = xyz ; use priodic BCs in all directions<br><br>; Run control<br>integrator = md ; type of dynamics algorithm. Here md uses a leap-frog algorithm for integrating Newtons's eq of motion<br>
dt = 0.002 ; in ps !<br>nsteps = 5000 ; length of simulation= nsteps*dt <br>nstcomm = 1 ; frequency for center of mass motion removal <br><br>
; Output control<br>nstenergy = 100 ; frequency to write energies to energy file. i.e., energies and other statistical data are stored every 10 steps<br>nstxout = 100 ; frequency to write coordinates/velocity/force to output trajectory file. how often snapshots are collected= nstxout*dt<br>
nstvout = 100<br>nstfout = 0<br>nstlog = 100 ; frequency to write energies to log file<br>nstxtcout = 10 ; frequency to write coordinates to xtc trajectory<br>
<br>; Neighbor searching<br>nstlist = 10 ; frequency to update neighbor list. Neighborlist will be updated at least every 10 steps. Manual p80<br>ns_type = grid ; make a grid in the box and only check atoms in neighboring grid cells when constructing a new neighbor list every nstlist steps<br>
<br>; Electrostatics/VdW<br>coulombtype = Shift ; tells gromacs how to model electrostatics. Coulomb/LJ potential is decreased over the whole range and forces decay smoothly to zero between <br>vdw-type = Shift ; rcoulomb-switch/rvw-switch & rcoulomb/rvdw<br>
rcoulomb-switch = 0 ; where to start switching the Coulomb potential <br>rvw-switch = 0 ; where to start switching the LJ potential <br><br>; Cut-offs<br>
rlist = 1.1 ; in nm. Cut-off distance for short-range neighbor list<br>rcoulomb = 1.0 ; distance for coulomb cut-off <br>rvdw = 1.0 ; distance for coulomb cut-off <br>
<br>; Temperature coupling <br>Tcoupl = berendsen<br>tc-grps = polymer ;HEX ; groups to couple to thermostat; Berendsen temperature coupling is on in these groups <br>
tau_t = 0.1 ;0.1 ; time constant for T coupling <br>ref_t = 300 ;300 ; reference T for coupling. When you alter the T, don't forget to change the gen_temp for velocity generation<br>
<br>; Pressure coupling<br>Pcoupl = berendsen ; Pressure coupling is not on<br>Pcoupltype = isotropic ; means the box expands and contracts in all directions (x,y,z) in order to maintain the proper pressure<br>
tau_p = 0.5 ; time constant for coupling in ps <br>compressibility = 4.5e-5 ; compressibility of solvent used in simulation in 1/bar<br>ref_p = 1.0 ; reference P for coupling in bar<br>
<br>; Velocity generation Generate velocites is on at 300 K. Manual p155<br>gen_vel = yes ; generate velocites according to Maxwell distribution at T: gen_temp with random gen seed gen_seed<br>
gen_temp = 300.0 ; T for Maxwell distribution <br>gen_seed = 173529 ; used to initialize random generator for random velocities<br><br>; Bonds<br>constraints = all-bonds ; sets the LINCS constraint for all bonds<br>
constraint-algorithm = lincs<br><br><br>