[gmx-users] Warnings related to Berendsen pressure coupling and use the refcoord_scaling option

PAVAN PAYGHAN pavanapex at gmail.com
Thu Jun 7 12:33:06 CEST 2012

 Dear Gromacs Users,

 I am using gromacs version 4.5.5.and running my jobs on single node with 8
cores. My system contains about 425000 atoms (protein + Lipid +SOL). I have
successfully reached up to Energy minimization step.As per the suggestion
by Dear Mark, I am starting my NPT equilibration with Berendsen and further
with Parinello-Rahman to get the right ensemble.But when I am trying for
NPT equilibration with Berendsen, getting following Warnings.

WARNING 1 [file npt.mdp]: Using Berendsen pressure coupling invalidates the
true ensemble for the thermostat

WARNING 2 [file npt.mdp]: You are using pressure coupling with absolute
position restraints, this will give artifacts.  Use the refcoord_scaling

 And about 10 such  LINCS warnings while running the job as shown below:

Step 39, time 0.078 (ps)  LINCS WARNING

relative constraint deviation after LINCS:

rms 0.000029, max 0.000473 (between atoms 890 and 891)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
  12050  12049   31.2    0.1000   0.1000      0.1000
  11721  11720   46.0    0.1000   0.1000      0.1000
   5496   5495   36.8    0.1000   0.1000      0.1000

 With –maxwarn option I am able to run it, and output density and pressure
seems perfectly alright.

Based on the same I want to know:-

   1. How does pressure coupling with Berendsen invalidates the true

At least for initial fixing of density and pressure?

Whether to bother for above mentioned warning or ignore it?

   1. Pressure coupling with absolute position restraints warning how it
   will lead to artifacts?

How one can use refcoord_scaling option in this situation?

Whether to bother for above mentioned warning or ignore it?

   1. Using Berendsen with semiisotropic couple type is wrong method or no
   such problem?

Please suggest me whether to move ahead with ignorance to the warnings or
to change some parameters in mdp file?

I have attached my npt.mdp file for your consideration.

Thanking you  In advance,

Pavan Payghan
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