Hai all....<br>
I am trying to simulate the bulk phase decane system using
GROMACS........... I used decane pdb file which I goT from HIC UP.... I
changed the residue name to C10 from D10 to match the residue name in
ffgmx.rtp(GROMACS force field)....<br>
I ran pdb2gmx , selected forcefield "4"(ffgmx)... and got .top and gro
files for my decane molecule...There saw the molecule mass as 142.17
which is correct ....... Now as I want to simulate Bulk I used
genconf to get my 512 molecule system..... i got out.gro file from
this..... To get the desired density I used editconf to get 602 gr/ltr
....But here in out put as shown below its showing the different mass
for 512 molecules i.e 61498.9.....(see output of editconf)......which
means that single molecule mass is 120.11.......means hydrogen masses
are missing....... I checked atommass.dat and I am unable to know
what I have to do..... <br>
<br>
Awaiting for help <br>
<br>
Arun<br>
<br>
GENCONF output<br>
<br clear="all">[arun@cluster ~]$ !genconf<br>
genconf -nbox 8 8 8 -dist 1 1 1 -f conf.gro<br>
:-) G R O M A C S (-:<br>
<br>
GROup of MAchos and Cynical Suckers<br>
<br>
:-) VERSION 3.2.1 (-:<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) 2001-2004, 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>
:-) genconf (-:<br>
<br>
Option Filename Type Description<br>
------------------------------------------------------------<br>
-f conf.gro
Input Generic structure: gro
g96 pdb tpr tpb tpa<br>
xml<br>
-o out.gro
Output Generic structure: gro g96
pdb xml<br>
-trj traj.xtc Input, Opt. Generic trajectory: xtc trr trj gro g96 pdb<br>
<br>
Option Type Value Description<br>
------------------------------------------------------<br>
-[no]h bool no Print help info and quit<br>
-[no]X
bool no Use dialog box GUI to edit
command line options<br>
-nice int 0 Set the nicelevel<br>
-nbox vector 8 8 8 Number of boxes<br>
-dist vector 1 1 1 Distance between boxes<br>
-seed
int 0 Random generator seed, if 0
generated from the<br>
time<br>
-[no]rot bool no Randomly rotate conformations<br>
-[no]shuffle bool no Random shuffling of molecules<br>
-[no]sort bool no Sort molecules on X coord<br>
-block
int 1 Divide the box in blocks on
this number of cpus<br>
-nmolat
int 3 Number of atoms per molecule,
assumed to start<br>
from 0. If you set this wrong, it will screw up<br>
your system!<br>
-maxrot vector 90 90 90 Maximum random rotation<br>
-[no]renumber bool no Renumber residues<br>
<br>
<br>
gcq#77: "One Cross Each" (Monty Python)<br>
<br>
###############################################################################<br>
After then I ran editconf to change density .............. I used 512
decane molecules... But I did not get the total mass of 512*142=72704
amu... Instead I got 61498.9 which is 512*120 that means hydrogen
masses are missing.... Can anyone help me in this
regard.........................<br>
##############################################################<br>
Here is the output................<br>
<br>
<br>
[arun@cluster ~]$ editconf -density 602 -f out.gro<br>
:-) G R O M A C S (-:<br>
<br>
Gromacs Runs On Most of All Computer Systems<br>
<br>
:-) VERSION 3.2.1 (-:<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) 2001-2004, 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>
:-) editconf (-:<br>
<br>
Option Filename Type Description<br>
------------------------------------------------------------<br>
-f out.gro
Input Generic structure: gro
g96 pdb tpr tpb tpa<br>
xml<br>
-n index.ndx Input, Opt. Index file<br>
-o out.gro
Output Generic structure: gro g96
pdb xml<br>
-bf bfact.dat Input, Opt. Generic data file<br>
<br>
Option Type Value Description<br>
------------------------------------------------------<br>
-[no]h bool no Print help info and quit<br>
-[no]X
bool no Use dialog box GUI to edit
command line options<br>
-nice int 0 Set the nicelevel<br>
-[no]w bool no View output xvg, xpm, eps and pdb files<br>
-[no]ndef bool no Choose output from default index groups<br>
-bt
enum tric Box type for -box and -d: tric, cubic,<br>
dodecahedron or octahedron<br>
-box vector 0 0 0 Box vector lengths (a,b,c)<br>
-angles vector 90 90 90 Angles between the box vectors (bc,ac,ab)<br>
-d
real 0 Distance between the solute
and the box<br>
-[no]c
bool no Center molecule in box (implied
by -box and -d)<br>
-center vector 0 0 0 Coordinates of geometrical center<br>
-translate vector 0 0 0 Translation<br>
-rotate vector 0 0 0 Rotation around the X, Y and Z axes in degrees<br>
-[no]princ bool no Orient molecule(s) along their principal axes<br>
-scale vector 1 1 1 Scaling factor<br>
-density real 602 Density (g/l) of the output box achieved by<br>
scaling<br>
-[no]vol bool yes Compute and print volume of the box<br>
-[no]pbc bool no Remove the periodicity (make molecule whole<br>
again)<br>
-[no]mead bool no Store the charge of the atom in the occupancy<br>
field and the radius of the atom in the B-factor<br>
field<br>
-[no]grasp bool no Store the charge of the atom in the B-factor<br>
field and the radius of the atom in the occupancy<br>
field<br>
-rvdw real
0.12 Default Van der Waals radius if one can not be<br>
found in the database<br>
-[no]atom bool no Force B-factor attachment per atom<br>
-[no]legend bool no Make B-factor legend<br>
-label string A Add chain label for all residues<br>
<br>
WARNING: masses will be determined based on residue and atom names,<br>
this can deviate from the real mass of the atom type<br>
In case you use free energy of solvation predictions:<br>
<br>
++++++++ PLEASE CITE THE FOLLOWING REFERENCE ++++++++<br>
D. Eisenberg and A. D. McLachlan<br>
Solvation energy in protein folding and binding<br>
Nature 319 (1986) pp. 199-203<br>
-------- -------- --- Thank You --- -------- --------<br>
<br>
Opening library file /opt/gromacs-3.2.1/share/top/aminoacids.dat<br>
Opening library file /opt/gromacs-3.2.1/share/top/atommass.dat<br>
Opening library file /opt/gromacs-3.2.1/share/top/vdwradii.dat<br>
Opening library file /opt/gromacs-3.2.1/share/top/dgsolv.dat<br>
#Entries in atommass.dat: 82 vdwradii.dat: 26 dgsolv.dat: 7<br>
Read 5120 atoms<br>
Volume: 1207.38 nm^3, corresponds to roughly 543300 electrons<br>
No velocities found<br>
system size : 16.008 7.874 7.000 (nm)<br>
center : 8.504 4.437 4.000 (nm)<br>
box vectors : 17.008 8.874 8.000 (nm)<br>
box angles : 90.00 90.00 90.00 (degrees)<br>
box volume
:1207.38
(nm^3)<br>
Volume of input 1207.38 (nm^3)<br>
Mass of input 61498.9 (a.m.u.)<br>
Density of input 84.5812 (g/l)<br>
Scaling all box vectors by 0.519867<br>
new system size : 8.322 4.093 3.639<br>
new center : 4.421 2.307 2.079 (nm)<br>
new box vectors : 8.842 4.613 4.159 (nm)<br>
new box angles : 90.00 90.00 90.00 (degrees)<br>
new box volume : 169.64 (nm^3)<br>
<br>
Back Off! I just backed up out.gro to ./#out.gro.1#<br>
<br>
gcq#267: "In the End Science Comes Down to Praying" (P. v.d. Berg)<br>
<br>
<br>
<br>
<br>
<br>-- <br>Arun kumar.V<br>M.E Chemical