[gmx-users] Incorrect number of parameters - found 3, expected 1 or 1 for Polarization.

[Justin Lemkul]

On 8/21/15 12:34 PM, 折晓会 wrote:
> Thank you professor Justin.
> Firstly, I get a true trajectory (stress.trr) from Gromacs 5.0.5 besides the water.gro, water.top, and nvt.mdp files. Then read the these files with a custom Gromacs 4.5.5 to calculate local pressure:
> grompp_LS  -f
> nvt.mdp  -c  water.gro
> -p  water.top  -o
> topol.tpr
>
> mdrun_LS    -s  topol.tpr   -rerun  stress.trr    -localsgrid
>   0.2   -lsgridx 1   -lsgridy 1
> The problem is when I set the box dimensions to be decimals (say 4.5 nm) in water.gro, the mdrun_LS does not work. After changing them to be integers (such as 4 or 5 nm), the mdrun_LS works. Will this affect the results? I am using the true trajectory (stress.trr) in -rerun command. What roles do the .gro and .mdp files play in the -rerun since positions and velocities of atoms at each frame are available in the .trr file?

Sorry, I don't know anything about the local pressure code. But what you're 
reporting sounds buggy to me, and circumventing it by randomly changing box 
vectors does not sound appropriate to me.

-Justin

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

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

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

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