On 7/06/2012 8:33 PM, PAVAN PAYGHAN wrote:
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 option.
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
ensemble?
See manual sections for T and P coupling for introductory discussion.
At least for initial fixing of density and pressure?
Whether to bother for above mentioned warning or ignore it?
Since you're going to do more equilibration after this, you be the judge.
2. Pressure coupling with absolute position restraints warning how it
will lead to artifacts?
How one can use refcoord_scaling option in this situation?
See manual.
Whether to bother for above mentioned warning or ignore it?
Position restraints and NPT is messy. Choose your poison.
3. 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?
That's your judgement to make. How does your preparation protocol
compare to the ones you have read about in the recent literature?
Mark
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
