[gmx-users] Regarding lipid bilayer simulation

Justin Lemkul jalemkul at vt.edu
Sun Oct 6 14:26:22 CEST 2013

On 10/6/13 12:47 AM, hasthi wrote:
> Dear GROMACS users,
>                                  I have been trying to simulate protein of
> my interest in lipid bilayer(POPC) . I am following the tutorial of KALP-15
> in DPPC. When I try to minimise the system after generating
> system_inflated.gro. I get a fatal error from grompp which reads invalid
> line in system_inflated.gro.
> I am trying to follow the tutorial KALP15 in DPPC for lipid bilayer
> simulation. When I minimise the system after generating
> system_inflated.gro, I get a fatal error as given below.
> Fatal error:
> Invalid line in system_inflated.gro for atom 6439:
>    25.67360  25.77400   6.59650
> 25.67360  25.77400   6.59650 (This is the box vectors which comes in the
> system_inflated.gro).I am clueless about this error.
> What might be the probable reason for this error?? Thanks in advance for
> the suggestions.

You have constructed system.gro incorrectly such that it specifies the wrong 
number of atoms on the second line.  grompp is still looking for atoms when it 
encounters the box vectors (end of the file).



Justin A. Lemkul, Ph.D.
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


More information about the gromacs.org_gmx-users mailing list