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? 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
npt.doc
Description: MS-Word document
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