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On 12/02/2011 12:51 PM, Rini Gupta wrote:
<blockquote
cite="mid:1297474129.S.27024.57182.F.H.WU1hcmsgQWJyYWhhbQBSZTogW2dteC11c2Vyc10gZ2VuYm94IGVycm9y.f4-234-124.1297475514.58610@webmail.rediffmail.com"
type="cite"><br>
Hello Mark,<br>
<br>
Thanks for the reply.<br>
<br>
I tried to first make a box using editconf<br>
editconf_d_mpi -f conf.gro -o be.gro -bt cubic -box 2.7 2.7 2.7<br>
<br>
Box is successfully created and then I use <br>
<br>
genbox_d_mpi -cp be.gro -p topol.top -ci be.gro -nmol 19 -o
out.gro<br>
<br>
still, I am getting only one BE molecule instead of 19.<br>
</blockquote>
<br>
Hmm that's strange. What was the terminal output?<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:1297474129.S.27024.57182.F.H.WU1hcmsgQWJyYWhhbQBSZTogW2dteC11c2Vyc10gZ2VuYm94IGVycm9y.f4-234-124.1297475514.58610@webmail.rediffmail.com"
type="cite"> What can I do now? Is there possibilty that my .gro
file is not correct.<br>
<br>
Best Regards,<br>
Rini<br>
<br>
On Sat, 12 Feb 2011 06:58:49 +0530 wrote<br>
><br>
<br>
<br>
<br>
<br>
On 12/02/2011 7:51 AM, Rini Gupta wrote:<br>
Dear gmx users,<br>
<br>
<br>
<br>
I am using gromacs (version 4.0.7) <br>
<br>
to setup a 2-butoxyethanol-water simulation.<br>
<br>
I created topology and coordinate file (.pdb) for BE using<br>
AUTOMATED TOPOLOGY BUILDER server.<br>
<br>
It created a topology file (for united atom) compatible with<br>
GROMOS ffG53a6 forcefield.<br>
<br>
I want to generate a box containing 20 BE and 480 water molecules<br>
using<br>
<br>
genbox but it fails to do so. It generates a box only with 1 BE<br>
instead of 20 but successfully adding requested no. of water<br>
molecules. <br>
<br>
<br>
<br>
I used the following command:<br>
<br>
<br>
<br>
<br>
<br>
genbox_d_mpi -cp conf.gro -cs spc216.gro -p topol.top -box 2.7 2.7<br>
2.7 -ci conf.gro -nmol 19 -maxsol 480 -o out.gro<br>
<br>
<br>
<br>
Then I got the mesaage:<br>
<br>
<br>
<br>
Reading solute configuration<br>
<br>
UNITED ATOM STRUCTURE FOR MOLECULE<br>
<br>
Containing 9 atoms in 1 residues<br>
<br>
Initialising van der waals distances...<br>
<br>
Reading molecule configuration <br>
<br>
UNITED ATOM STRUCTURE FOR MOLECULE<br>
<br>
Containing 9 atoms in 1 residue<br>
<br>
Initialising van der waals distances...<br>
<br>
Try 5699<br>
<br>
Added 0 molecules (out of 19 requested) of G2<br>
<br>
Reading solvent configuration<br>
<br>
"216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR.<br>
1984"<br>
<br>
solvent configuration contains 648 atoms in 216 residues<br>
<br>
<br>
<br>
Initialising van der waals distances...<br>
<br>
Will generate new solvent configuration of 2x2x2 boxes<br>
<br>
Generating configuration<br>
<br>
Sorting configuration<br>
<br>
Found 1 molecule type:<br>
<br>
SOL ( 3 atoms): 1728 residues<br>
<br>
Calculating Overlap...<br>
<br>
box_margin = 0.315<br>
<br>
Removed 1992 atoms that were outside the box<br>
<br>
Neighborsearching with a cut-off of 0.45<br>
<br>
Table routines are used for coulomb: FALSE<br>
<br>
Table routines are used for vdw: FALSE<br>
<br>
Cut-off's: NS: 0.45 Coulomb: 0.45 LJ: 0.45<br>
<br>
System total charge: 0.000<br>
<br>
Grid: 8 x 8 x 8 cells<br>
<br>
Succesfully made neighbourlist<br>
<br>
nri = 10648, nrj = 270745<br>
<br>
Checking Protein-Solvent overlap: tested 509 pairs, removed 72<br>
atoms.<br>
<br>
Checking Solvent-Solvent overlap: tested 39413 pairs, removed 738<br>
atoms.<br>
<br>
Added 480 molecules<br>
<br>
Generated solvent containing 1440 atoms in 480 residues<br>
<br>
Writing generated configuration to out.gro<br>
<br>
<br>
<br>
<br>
<br>
While searching through mailing list I tried to do this in two<br>
separate steps i.e. but using -ci -nmol option and then solvating<br>
the box using -cs spc216.gro, but problem remain the same.<br>
<br>
I also tried increasing -try option and increasing the box size<br>
but still it is creating box with only one solute BE instead od<br>
20.<br>
<br>
<br>
<br>
<br>
You're definitely trying to do too many things in one operation. I<br>
suggest<br>
<br>
<br>
<br>
1. Use editconf to define a suitably big box around a single BE<br>
molecule.<br>
<br>
<br>
<br>
2. Use genbox -ci -nmol 19<br>
<br>
<br>
<br>
3. Use genbox -cs -cp<br>
<br>
<br>
<br>
Or use genconf -shuffle to replace 1 and 2 (but this is less
random)<br>
<br>
<br>
<br>
Mark<br>
<br>
<br>
<br>
<br>
<br>
<br>
Can anyone please tell me what I am doing wrong here.<br>
<br>
<br>
<br>
I using following topology file:<br>
<br>
<br>
<br>
[ moleculetype ]<br>
<br>
; Name nrexcl<br>
<br>
G269 3<br>
<br>
[ atoms ]<br>
<br>
; nr type resnr resid atom cgnr charge mass total_charge<br>
<br>
1 OE 1 G2 OE 1 -0.345 15.9994<br>
<br>
2 CH2 1 G2 C 1 0.151 14.0270<br>
<br>
3 CH2 1 G2 C 1 0.194 14.0270 ; 0.000<br>
<br>
4 CH2 1 G2 C 2 0.231 14.0270<br>
<br>
5 OA 1 G2 O 2 -0.617 15.9994<br>
<br>
6 H 1 G2 H 2 0.386 1.0080 ; 0.000<br>
<br>
7 CH2 1 G2 C 3 -0.035 14.0270<br>
<br>
8 CH2 1 G2 C 3 0.143 14.0270<br>
<br>
9 CH3 1 G2 CA 3 -0.108 15.0350 ; -0.000<br>
<br>
; total charge of the molecule: 0.000<br>
<br>
[ bonds ]<br>
<br>
; ai aj funct c0 c1<br>
<br>
1 2 2 0.1430 8.1800e+06<br>
<br>
1 3 2 0.1430 8.1800e+06<br>
<br>
2 4 2 0.1520 5.4300e+06<br>
<br>
3 7 2 0.1520 5.4300e+06<br>
<br>
4 5 2 0.1430 8.1800e+06<br>
<br>
5 6 2 0.1000 2.3200e+07<br>
<br>
7 8 2 0.1530 7.1500e+06<br>
<br>
8 9 2 0.1530 7.1500e+06<br>
<br>
[ pairs ]<br>
<br>
; ai aj funct ; all 1-4 pairs but the ones excluded in GROMOS itp<br>
<br>
1 5 1<br>
<br>
1 8 1<br>
<br>
2 6 1<br>
<br>
2 7 1<br>
<br>
3 4 1<br>
<br>
3 9 1<br>
<br>
[ angles ]<br>
<br>
; ai aj ak funct angle fc<br>
<br>
2 1 3 2 109.50 380.00<br>
<br>
1 2 4 2 109.50 320.00<br>
<br>
1 3 7 2 109.50 320.00<br>
<br>
2 4 5 2 111.00 530.00<br>
<br>
4 5 6 2 108.53 443.00<br>
<br>
3 7 8 2 111.00 530.00<br>
<br>
7 8 9 2 111.00 530.00<br>
<br>
[ dihedrals ]<br>
<br>
; GROMOS improper dihedrals<br>
<br>
; ai aj ak al funct angle fc<br>
<br>
[ dihedrals ]<br>
<br>
; ai aj ak al funct ph0 cp mult<br>
<br>
3 1 2 4 1 0.00 1.26 3<br>
<br>
2 1 3 7 1 0.00 1.26 3<br>
<br>
1 2 4 5 1 0.00 2.53 3<br>
<br>
1 3 7 8 1 0.00 3.77 3<br>
<br>
2 4 5 6 1 0.00 1.26 3<br>
<br>
3 7 8 9 1 0.00 3.77 3<br>
<br>
[ exclusions ]<br>
<br>
; ai aj funct ; GROMOS 1-4 exclusions<br>
<br>
<br>
<br>
<br>
<br>
Thanks and Regards,<br>
<br>
Rini<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
----------------<br>
<br>
Dr. Rini Gupta<br>
<br>
Postdoctoral Fellow<br>
<br>
University of British Columbia<br>
<br>
Vancouver<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
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<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
-- <br>
<br>
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