[gmx-users] Cyclohexane simulation problem

[mohsen shahlaei]

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)

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.


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