[gmx-users] guanidinium in water

[Swetha Srinivasan]

Hi Lemkul,

I had already used a rhein-water system before. I just edited that and gave my inputs.

Thanks,

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 12:03 PM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] guanidinium in water

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

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

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