Dear gmx users,<br />
<br />
I am using gromacs (version 4.0.7) <br />
to setup a 2-butoxyethanol-water simulation.<br />
I created topology and coordinate file (.pdb) for BE using AUTOMATED TOPOLOGY BUILDER server.<br />
It created a topology file (for united atom) compatible with GROMOS ffG53a6 forcefield.<br />
I want to generate a box containing 20 BE and 480 water molecules using<br />
genbox but it fails to do so. It generates a box only with 1 BE instead of 20 but successfully adding requested no. of water molecules. <br />
<br />
I used the following command:<br />
<br />
<br />
genbox_d_mpi -cp conf.gro -cs spc216.gro -p topol.top -box 2.7 2.7 2.7 -ci conf.gro -nmol 19 -maxsol 480 -o out.gro<br />
<br />
Then I got the mesaage:<br />
<br />
Reading solute configuration<br />
UNITED ATOM STRUCTURE FOR MOLECULE<br />
Containing 9 atoms in 1 residues<br />
Initialising van der waals distances...<br />
Reading molecule configuration <br />
UNITED ATOM STRUCTURE FOR MOLECULE<br />
Containing 9 atoms in 1 residue<br />
Initialising van der waals distances...<br />
Try 5699<br />
Added 0 molecules (out of 19 requested) of G2<br />
Reading solvent configuration<br />
"216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984"<br />
solvent configuration contains 648 atoms in 216 residues<br />
<br />
Initialising van der waals distances...<br />
Will generate new solvent configuration of 2x2x2 boxes<br />
Generating configuration<br />
Sorting configuration<br />
Found 1 molecule type:<br />
SOL ( 3 atoms): 1728 residues<br />
Calculating Overlap...<br />
box_margin = 0.315<br />
Removed 1992 atoms that were outside the box<br />
Neighborsearching with a cut-off of 0.45<br />
Table routines are used for coulomb: FALSE<br />
Table routines are used for vdw: FALSE<br />
Cut-off's: NS: 0.45 Coulomb: 0.45 LJ: 0.45<br />
System total charge: 0.000<br />
Grid: 8 x 8 x 8 cells<br />
Succesfully made neighbourlist<br />
nri = 10648, nrj = 270745<br />
Checking Protein-Solvent overlap: tested 509 pairs, removed 72 atoms.<br />
Checking Solvent-Solvent overlap: tested 39413 pairs, removed 738 atoms.<br />
Added 480 molecules<br />
Generated solvent containing 1440 atoms in 480 residues<br />
Writing generated configuration to out.gro<br />
<br />
<br />
While searching through mailing list I tried to do this in two separate steps i.e. but using -ci -nmol option and then solvating the box using -cs spc216.gro, but problem remain the same.<br />
I also tried increasing -try option and increasing the box size but still it is creating box with only one solute BE instead od 20.<br />
<br />
Can anyone please tell me what I am doing wrong here.<br />
<br />
I using following topology file:<br />
<br />
[ moleculetype ]<br />
; Name nrexcl<br />
G269 3<br />
[ atoms ]<br />
; nr type resnr resid atom cgnr charge mass total_charge<br />
1 OE 1 G2 OE 1 -0.345 15.9994<br />
2 CH2 1 G2 C 1 0.151 14.0270<br />
3 CH2 1 G2 C 1 0.194 14.0270 ; 0.000<br />
4 CH2 1 G2 C 2 0.231 14.0270<br />
5 OA 1 G2 O 2 -0.617 15.9994<br />
6 H 1 G2 H 2 0.386 1.0080 ; 0.000<br />
7 CH2 1 G2 C 3 -0.035 14.0270<br />
8 CH2 1 G2 C 3 0.143 14.0270<br />
9 CH3 1 G2 CA 3 -0.108 15.0350 ; -0.000<br />
; total charge of the molecule: 0.000<br />
[ bonds ]<br />
; ai aj funct c0 c1<br />
1 2 2 0.1430 8.1800e+06<br />
1 3 2 0.1430 8.1800e+06<br />
2 4 2 0.1520 5.4300e+06<br />
3 7 2 0.1520 5.4300e+06<br />
4 5 2 0.1430 8.1800e+06<br />
5 6 2 0.1000 2.3200e+07<br />
7 8 2 0.1530 7.1500e+06<br />
8 9 2 0.1530 7.1500e+06<br />
[ pairs ]<br />
; ai aj funct ; all 1-4 pairs but the ones excluded in GROMOS itp<br />
1 5 1<br />
1 8 1<br />
2 6 1<br />
2 7 1<br />
3 4 1<br />
3 9 1<br />
[ angles ]<br />
; ai aj ak funct angle fc<br />
2 1 3 2 109.50 380.00<br />
1 2 4 2 109.50 320.00<br />
1 3 7 2 109.50 320.00<br />
2 4 5 2 111.00 530.00<br />
4 5 6 2 108.53 443.00<br />
3 7 8 2 111.00 530.00<br />
7 8 9 2 111.00 530.00<br />
[ dihedrals ]<br />
; GROMOS improper dihedrals<br />
; ai aj ak al funct angle fc<br />
[ dihedrals ]<br />
; ai aj ak al funct ph0 cp mult<br />
3 1 2 4 1 0.00 1.26 3<br />
2 1 3 7 1 0.00 1.26 3<br />
1 2 4 5 1 0.00 2.53 3<br />
1 3 7 8 1 0.00 3.77 3<br />
2 4 5 6 1 0.00 1.26 3<br />
3 7 8 9 1 0.00 3.77 3<br />
[ exclusions ]<br />
; ai aj funct ; GROMOS 1-4 exclusions<br />
<br />
<br />
Thanks and Regards,<br />
Rini<br />
<br />
<br />
<br />
----------------<br />
Dr. Rini Gupta<br />
Postdoctoral Fellow<br />
University of British Columbia<br />
Vancouver<br />
<br />
<br />
<br />
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