On 4/27/14, 11:57 AM, Swetha Srinivasan wrote:
Hi Lemkul,
genbox -cp test.gro -cs spc216.gro -box 24 24 24 -o watGND.gro
Actually I want to do a simulation for 7M concentration. So, since the conc of
3M is already done, I did a small calculation of mass of 3M/avogadro number =
7M* Mixed mass(Mgnd+Mcl/ratio)*V .From this,I got the volume.From this, the box
size was 24 24 24 . Thus I used this in the genbox.
Gromacs uses nm for all lengths and distances; I strongly suspect you assumed it
was A. The topology section below definitely does not correspond to 7 M.
Output configuration contains 1384837 atoms in 461568 residues
Volume : 13824 (nm^3)
Density : 998.941 (g/l)
Number of SOL molecules: 461549
Next,grompp command
grompp -f ions.mdp -c watGND.gro -p system.top -o ions.tpr
My system.top file
#include "gromos43a1.ff/forcefield.itp"
#include "spc.itp"
#include "gnd.itp"
[ molecule ]
; Name
guanidium in water
[ molecule ]
; Compound #molecule
GND 19
SOL 461549
CL- 38
~
My ions.mdp file
ions.mdp - used as input into grompp to generate ions.tpr
; RUN CONTROL PARAMETERS
integrator = md
; Start time and timestep in ps
tinit = 0
dt = 0.001
nsteps = 0
; For exact run continuation or redoing part of a run
init_step = 0
; Part index is updated automatically on checkpointing (keeps files separate)
simulation_part = 1
; mode for center of mass motion removal
comm-mode = Linear
; number of steps for center of mass motion removal
nstcomm = 10
; group(s) for center of mass motion removal
comm-grps =
; LANGEVIN DYNAMICS OPTIONS
; Friction coefficient (amu/ps) and random seed
bd-fric = 0
ld-seed = 1993
grompp -f ions.mdp -c watGND.gro -p system.top -o ions.tpr
Program grompp, VERSION 4.5.5
Source code file: toppush.c, line: 1631
Fatal error:
Incorrect number of parameters - found 2, expected 5 or 5 for LJC-14 q.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
This is the trouble Im facing. Hoping for a positive reply soon.
OK, so you're specifying type-2 pairs. Again I ask: what is the source of this
topology? Do you really intend to use this interaction? This pair type is
rather unusual and requires you to specify van der Waals parameters (V, W) and
charges (qi, qj), as well as fudge factor for the interactions (fudgeQQ) - hence
5 parameters.
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
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