[gmx-users] Re: grompp for minimization: note & warning

[shahab shariati]

Dear Justin

Thanks for your reply


> You're still working with outdated software.  Please follow my
> suggestion of trying 4.6.3.

I try to install 4.6.3.

> The larger issue, in the end, is the unphysical configuration of the drug
> in the membrane.  Independent of Gromacs version, that setup will
> always fail.

I did minimization in 2 other states:

1) without drug (only membrane: DOPC nad cholesterol).

2) with drug but, this time, I put drug into water molecules not into
membrane.

Then I did mdrun for both of states. In both of state, there are not
following issues:

Warning: 1-4 interaction between 434 and 407 at distance 3.023 which is
larger than the 1-4 table size 2.200 nm These are ignored for the rest of
the simulation This usually means your system is exploding,

if not, you should increase table-extension in your mdp file
or with user tables increase the table size

step 23: Water molecule starting at atom 10613 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Wrote pdb files with previous and current coordinates

--------------------------------------------------------------------------
There are following outputs:

for state 1)
-------------

Reading file em.tpr, VERSION 4.5.1 (single precision)
Starting 4 threads
Making 2D domain decomposition 1 x 2 x 2

Steepest Descents:
   Tolerance (Fmax)   =  1.00000e+03
   Number of steps    =        50000

Stepsize too small, or no change in energy.
Converged to machine precision,
but not to the requested precision Fmax < 1000

Double precision normally gives you higher accuracy.
You might need to increase your constraint accuracy, or turn
off constraints alltogether (set constraints = none in mdp file)

writing lowest energy coordinates.

Steepest Descents converged to machine precision in 881 steps,
but did not reach the requested Fmax < 1000.
Potential Energy  =  2.1828770e+05
Maximum force     =  1.3656898e+04 on atom 618
Norm of force     =  5.1748779e+02
--------------------------------------------------------------------

for state 2)
----------------

Reading file em.tpr, VERSION 4.5.1 (single precision)
Starting 4 threads
Making 2D domain decomposition 1 x 2 x 2

Back Off! I just backed up em.trr to ./#em.trr.1#

Back Off! I just backed up em.edr to ./#em.edr.1#

Steepest Descents:
   Tolerance (Fmax)   =  1.00000e+03
   Number of steps    =        50000

Stepsize too small, or no change in energy.
Converged to machine precision,
but not to the requested precision Fmax < 1000

Double precision normally gives you higher accuracy.
You might need to increase your constraint accuracy, or turn
off constraints alltogether (set constraints = none in mdp file)

writing lowest energy coordinates.

Back Off! I just backed up em.gro to ./#em.gro.1#

Steepest Descents converged to machine precision in 845 steps,
but did not reach the requested Fmax < 1000.
Potential Energy  =  1.9664772e+05
Maximum force     =  1.0986521e+04 on atom 241
Norm of force     =  4.4174323e+02
---------------------------------------------------------------------------

When I see created gro file from minimization (em.gro), I see some dopc and
cholesterol molecules were broken and they devided 2 or 3 parts. Input gro
file (system.gro) has 1835 residues. Created gro file from minimization
(em.gro) has 1835 residues. But when I load em.gro file in VMD, there are
1950 residues in graphical representation --> selections --> residues part.

Can I deduce my problem has not dependent to presence of drug?

Are there problem about my force field parameters or topology file ?

I get force field parameters from lipid book (for dopc and cholesterol) and
from prodrg server (for drug).

Please help me to resolve this issue.

Best wishes for you