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

[折晓会]

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? 
Best wishes,Xiaohui


> Date: Thu, 20 Aug 2015 18:52:05 -0400
> From: jalemkul at vt.edu
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Incorrect number of parameters - found 3, expected 1 or 1 for Polarization.
> 
> 
> 
> On 8/20/15 6:05 PM, 折晓会 wrote:
> > Thank you professor Justin! I solved this error which comes from the decimals of the box dimensions. Initially, my box dimensions are 4.5*4.5*16 nm3 and the local pressure calculation does not work, but after I change them to be integers 4*4*16 nm3 in the gro file, the simulation works. It is strange for me. I do not know why.
> >
> 
> I fail to see how making the box smaller solves a "box too small" error, and 
> moreover, making changes like this is going to affect the results.  Don't 
> consider this a solution.  Probably an indication of a bug.  So you're just 
> reading in a .gro file?  Does a single coordinate file trigger the error before, 
> or was that from an actual trajectory?
> 
> -Justin
> 
> > Best wishes,
> > Xiaohui
> >
> >> Date: Thu, 20 Aug 2015 16:44:58 -0400
> >> From: jalemkul at vt.edu
> >> To: gmx-users at gromacs.org
> >> Subject: Re: [gmx-users] Incorrect number of parameters - found 3, expected 1 or 1 for Polarization.
> >>
> >>
> >>
> >> On 8/20/15 4:01 PM, 折晓会 wrote:
> >>> Thank you professor Justin! I solved this error with your suggestion.
> >>>
> >>> When I use mdrun -rerun to calculate the local pressure, another error occurs:
> >>>
> >>> Fatal error:
> >>> Rerun trajectory frame step 600000 time 600.000000 has too small box dimensions
> >>>
> >>> What does this mean?
> >>>
> >>
> >> It means your box is too small.  What are the box dimensions in that frame, and
> >> what are the cutoffs you are using?
> >>
> >> -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
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> -- 
> ==================================================
> 
> 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
> 
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