[gmx-users] guanidinium in water

[Swetha Srinivasan]

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. 

    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.

Regards,

Swetha


________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Justin Lemkul <jalemkul at vt.edu>
Sent: Sunday, April 27, 2014 11:38 AM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] guanidinium in water

Please don't hijack an unrelated thread with a new question.  I am re-titling
this message; in the future, just send a new email when you have a new question.

On 4/27/14, 11:11 AM, Swetha Srinivasan wrote:
> Hi Lemkul,
>
> I am trying to simulate guanidium in water. My system contains 198 guanidium residues. But when I'm trying to use the grompp command ,I'm facing the problem of fudgeQQ, qi ,qj. I don't know what that means. I don't know how to rectify the error too. Plus if there are too many solvet molecules, how do I delete it ?
>

FudgeQQ is explained in the manual.  Beyond that, you need to provide more
details.  What is in your topology?  Did you create it yourself, or did you get
it from some other source?  What is the *exact* error message from grompp
(copied and pasted from the terminal)?

As for solvent removal, you'll have to tell us how you added solvent in the
first place.  Presumably this was done with genbox, in which case you can use
-maxsol, but that's often not a good idea because it will leave voids in the
simulation box.  If the box is too large, you'll have to set up an appropriate
one with editconf (or possibly genbox, but I'm still guessing here because you
haven't provided any of your commands).

-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

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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