On 12/02/2011 12:51 PM, Rini Gupta wrote:
Hello Mark,
Thanks for the reply.
I tried to first make a box using editconf
editconf_d_mpi -f conf.gro -o be.gro -bt cubic -box 2.7 2.7 2.7
Box is successfully created and then I use
genbox_d_mpi -cp be.gro -p topol.top -ci be.gro -nmol 19 -o out.gro
still, I am getting only one BE molecule instead of 19.
Hmm that's strange. What was the terminal output?
Mark
What can I do now? Is there possibilty that my .gro file is not correct.
Best Regards,
Rini
On Sat, 12 Feb 2011 06:58:49 +0530 wrote
>
On 12/02/2011 7:51 AM, Rini Gupta wrote:
Dear gmx users,
I am using gromacs (version 4.0.7)
to setup a 2-butoxyethanol-water simulation.
I created topology and coordinate file (.pdb) for BE using
AUTOMATED TOPOLOGY BUILDER server.
It created a topology file (for united atom) compatible with
GROMOS ffG53a6 forcefield.
I want to generate a box containing 20 BE and 480 water molecules
using
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.
I used the following command:
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
Then I got the mesaage:
Reading solute configuration
UNITED ATOM STRUCTURE FOR MOLECULE
Containing 9 atoms in 1 residues
Initialising van der waals distances...
Reading molecule configuration
UNITED ATOM STRUCTURE FOR MOLECULE
Containing 9 atoms in 1 residue
Initialising van der waals distances...
Try 5699
Added 0 molecules (out of 19 requested) of G2
Reading solvent configuration
"216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR.
1984"
solvent configuration contains 648 atoms in 216 residues
Initialising van der waals distances...
Will generate new solvent configuration of 2x2x2 boxes
Generating configuration
Sorting configuration
Found 1 molecule type:
SOL ( 3 atoms): 1728 residues
Calculating Overlap...
box_margin = 0.315
Removed 1992 atoms that were outside the box
Neighborsearching with a cut-off of 0.45
Table routines are used for coulomb: FALSE
Table routines are used for vdw: FALSE
Cut-off's: NS: 0.45 Coulomb: 0.45 LJ: 0.45
System total charge: 0.000
Grid: 8 x 8 x 8 cells
Succesfully made neighbourlist
nri = 10648, nrj = 270745
Checking Protein-Solvent overlap: tested 509 pairs, removed 72
atoms.
Checking Solvent-Solvent overlap: tested 39413 pairs, removed 738
atoms.
Added 480 molecules
Generated solvent containing 1440 atoms in 480 residues
Writing generated configuration to out.gro
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.
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.
You're definitely trying to do too many things in one operation. I
suggest
1. Use editconf to define a suitably big box around a single BE
molecule.
2. Use genbox -ci -nmol 19
3. Use genbox -cs -cp
Or use genconf -shuffle to replace 1 and 2 (but this is less random)
Mark
Can anyone please tell me what I am doing wrong here.
I using following topology file:
[ moleculetype ]
; Name nrexcl
G269 3
[ atoms ]
; nr type resnr resid atom cgnr charge mass total_charge
1 OE 1 G2 OE 1 -0.345 15.9994
2 CH2 1 G2 C 1 0.151 14.0270
3 CH2 1 G2 C 1 0.194 14.0270 ; 0.000
4 CH2 1 G2 C 2 0.231 14.0270
5 OA 1 G2 O 2 -0.617 15.9994
6 H 1 G2 H 2 0.386 1.0080 ; 0.000
7 CH2 1 G2 C 3 -0.035 14.0270
8 CH2 1 G2 C 3 0.143 14.0270
9 CH3 1 G2 CA 3 -0.108 15.0350 ; -0.000
; total charge of the molecule: 0.000
[ bonds ]
; ai aj funct c0 c1
1 2 2 0.1430 8.1800e+06
1 3 2 0.1430 8.1800e+06
2 4 2 0.1520 5.4300e+06
3 7 2 0.1520 5.4300e+06
4 5 2 0.1430 8.1800e+06
5 6 2 0.1000 2.3200e+07
7 8 2 0.1530 7.1500e+06
8 9 2 0.1530 7.1500e+06
[ pairs ]
; ai aj funct ; all 1-4 pairs but the ones excluded in GROMOS itp
1 5 1
1 8 1
2 6 1
2 7 1
3 4 1
3 9 1
[ angles ]
; ai aj ak funct angle fc
2 1 3 2 109.50 380.00
1 2 4 2 109.50 320.00
1 3 7 2 109.50 320.00
2 4 5 2 111.00 530.00
4 5 6 2 108.53 443.00
3 7 8 2 111.00 530.00
7 8 9 2 111.00 530.00
[ dihedrals ]
; GROMOS improper dihedrals
; ai aj ak al funct angle fc
[ dihedrals ]
; ai aj ak al funct ph0 cp mult
3 1 2 4 1 0.00 1.26 3
2 1 3 7 1 0.00 1.26 3
1 2 4 5 1 0.00 2.53 3
1 3 7 8 1 0.00 3.77 3
2 4 5 6 1 0.00 1.26 3
3 7 8 9 1 0.00 3.77 3
[ exclusions ]
; ai aj funct ; GROMOS 1-4 exclusions
Thanks and Regards,
Rini
----------------
Dr. Rini Gupta
Postdoctoral Fellow
University of British Columbia
Vancouver
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
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://sigads.rediff.com/RealMedia/ads/click_nx.ads/www.rediffmail.com/signatureline.htm@Middle?>
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
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
