[gmx-users] Cyclohexane simulation problem

[Justin Lemkul]

On 5/30/15 3:44 AM, mohsen shahlaei wrote:
> Dear All, I am interested in simulation of cyclohexane box based on Lemkul tutorial. At first I built a box  using following commandgmx insert-molecules -ci chx.gro -nmol 500 -box 2.154434 2.154434 2.154434 -o chx_box.gro (I want a box with 10 nm3 volume)after run several times and convergence I have a box with 88 CHX.
> then I minimized energy using following mdp file:====================; minim.mdp - used as input into grompp to generate em.tpr
> integrator    = steep        ; Algorithm (steep = steepest descent minimization)
> emtol        = 100.0      ; Stop minimization when the maximum force < 1000.0 kJ/mol/nm
> emstep      = 0.01      ; Energy step size
> nsteps        = 500000          ; Maximum number of (minimization) steps to perform
>
> ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions
> nstlist            = 1            ; Frequency to update the neighbor list and long range forces
> cutoff-scheme   = Verlet
> ns_type            = grid        ; Method to determine neighbor list (simple, grid)
> coulombtype        = PME        ; Treatment of long range electrostatic interactions
> rcoulomb        = 1        ; Short-range electrostatic cut-off
> rvdw            = 1        ; Short-range Van der Waals cut-off
> pbc                = xyz         ; Periodic Boundary Conditions (yes/no)==================================================
>
> OOPS!! I got following fatal error
> =============
> GROMACS:      gmx grompp, VERSION 5.0.4
> Executable:   /usr/local/gromacs/bin/gmx
> Library dir:  /usr/local/gromacs/share/gromacs/top
> Command line:
>    gmx grompp -f minim.mdp -c chx_box.gro -p chx_box.top -o em.tpr
>
>
> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.41#
>
> NOTE 1 [file minim.mdp]:
>    With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
>    that with the Verlet scheme, nstlist has no effect on the accuracy of
>    your simulation.
>
> Setting the LD random seed to 1763529642
> Generated 165 of the 1596 non-bonded parameter combinations
> Excluding 3 bonded neighbours molecule type 'chx'
> Warning: atom name 1 in chx_box.top and chx_box.gro does not match (CAA - AA)
> Warning: atom name 2 in chx_box.top and chx_box.gro does not match (CAB - AB)
> Warning: atom name 3 in chx_box.top and chx_box.gro does not match (CAE - AE)
> Warning: atom name 4 in chx_box.top and chx_box.gro does not match (CAF - AF)
> Warning: atom name 5 in chx_box.top and chx_box.gro does not match (CAD - AD)
> Warning: atom name 6 in chx_box.top and chx_box.gro does not match (CAC - AC)
> Warning: atom name 7 in chx_box.top and chx_box.gro does not match (CAA - AA)
> Warning: atom name 8 in chx_box.top and chx_box.gro does not match (CAB - AB)
> Warning: atom name 9 in chx_box.top and chx_box.gro does not match (CAE - AE)
> Warning: atom name 10 in chx_box.top and chx_box.gro does not match (CAF - AF)
> Warning: atom name 11 in chx_box.top and chx_box.gro does not match (CAD - AD)
> Warning: atom name 12 in chx_box.top and chx_box.gro does not match (CAC - AC)
> Warning: atom name 13 in chx_box.top and chx_box.gro does not match (CAA - AA)
> Warning: atom name 14 in chx_box.top and chx_box.gro does not match (CAB - AB)
> Warning: atom name 15 in chx_box.top and chx_box.gro does not match (CAE - AE)
> Warning: atom name 16 in chx_box.top and chx_box.gro does not match (CAF - AF)
> Warning: atom name 17 in chx_box.top and chx_box.gro does not match (CAD - AD)
> Warning: atom name 18 in chx_box.top and chx_box.gro does not match (CAC - AC)
> Warning: atom name 19 in chx_box.top and chx_box.gro does not match (CAA - AA)
> Warning: atom name 20 in chx_box.top and chx_box.gro does not match (CAB - AB)
> (more than 20 non-matching atom names)
>

This suggests bad formatting of your input.  You've got a column shifted 
somewhere.  Make sure that isn't impacting the interpretation of the 
coordinates, which could be nonsense if they are similarly affected.

> WARNING 1 [file chx_box.top, line 58]:
>    528 non-matching atom names
>    atom names from chx_box.top will be used
>    atom names from chx_box.gro will be ignored
>
>
> Removing all charge groups because cutoff-scheme=Verlet
> Analysing residue names:
> There are:    88      Other residues
> Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
> Number of degrees of freedom in T-Coupling group rest is 1581.00
>
> WARNING 2 [file minim.mdp]:
>    You are using full electrostatics treatment PME for a system without
>    charges.
>    This costs a lot of performance for just processing zeros, consider using
>    Cut-off instead.
>

grompp is trying to help you out.  Change the coulombtype setting accordingly. 
You have no charges in a UA cyclohexane model, so the electrostatics method is 
totally irrelevant.

-Justin

>
> Calculating fourier grid dimensions for X Y Z
> Using a fourier grid of 20x20x20, spacing 0.108 0.108 0.108
> Estimate for the relative computational load of the PME mesh part: 0.23
> This run will generate roughly 2 Mb of data
>
> There was 1 note
>
> There were 2 warnings
>
> -------------------------------------------------------
> Program gmx, VERSION 5.0.4
> Source code file: /home/mohsen/Downloads/gromacs-5.0.4/src/gromacs/gmxpreprocess/grompp.c, line: 2087
>
> Fatal error:
> Too many warnings (2), gmx terminated.
> If you are sure all warnings are harmless, use the -maxwarn option.
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> =============================================
> any suggestion is appreciated
> best,
>
> Mohsen
>

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

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

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