[gmx-users] water simulation

[Justin A. Lemkul]

abhijit kayal wrote:

<snip>

> -------------------------------------------------------
> Program grompp, VERSION 4.0.4
> Source code file: topio.c, line: 415
> 
> Fatal error:
> Syntax error - File topol.top, line 4
> Last line read:
> '[ atomtypes ]'
> Invalid order for directive atomtypes
> -------------------------------------------------------

The topology file follows a specified format.  Refer to Chapter 5, especially 
Table 5.3 which spells out exactly which sections of the topology are mandatory, 
and the order they must be in.

> 
> "I believe in miracles cause I'm one" (The Ramones)
> 
> [abhijit at SCFBioServer gromacs]$
>  my topol.top file is
> xirs    fudgeLJ fudgeQQ
> 1               2               yes             0.5     0.5

At the very least, you're missing a [ defaults ] heading; otherwise these lines 
are incorrectly formatted.

> [ atomtypes ]
> ;name  at.num   mass       charge   ptype   sigma   epsilon
>   OW    8       15.99940   0.000    A       0.3166    0.65
>   HW    1        1.00800   0.000    A       0.00000E+00   0.00000E+00
> 

<snip>

> coulombtype              = Cut-off

Using cutoff for electrostatics is archaic, and the artefacts are well-known. 
Use something more modern like PME.

-Justin

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================