[gmx-users] free energy calculation: combination of position restraint +refcoord_scaling cause crash during NPT

Justin Lemkul jalemkul at vt.edu
Wed Feb 18 13:42:41 CET 2015

On 2/17/15 12:31 PM, Jin Zhang wrote:
> Dear all,
> We're doing free energy calculation and found some of my lambda job crashes
> due to the combination of position restraint +refcoord_scaling COM. All
> crashes happened at NPT steps.
> By checking each energy term, we found the Position Rest. term is
> surprisingly as high as 10^6 kJ/mol, the others look fine. Either turn of
> position restrain or refcoord_scaling could avoid the simulation to be
> crashed. We tried to see if there's mismatch of either COM or coordinate
> and found no direct answer.
> Any help would be appreciated!
> In the tpr file
>        refcoord-scaling     = COM
>        posres-com (3):
>        posres-com[0]= 3.15034e-01
>        posres-com[1]= 4.48110e-01
>        posres-com[2]= 5.17730e-01
> COM of protein-ligand calculated by t_traj -com -ox
> 3.02422    4.30169    4.84964

If the reference COM is defined as (0.315,0.448,0.518) and your actual 
coordinates are what you're shown above, there will inherently be a huge 
restraint potential as mdrun tries to bias the coordinates towards the defined 
reference.  I suspect something is wrong in your definition of your reference.


> coordinate of 1st atom in tpr: posres_xA[    0]={ 1.39783e-01,
> -9.56922e-02,  1.22536e+00}
> coordinate of 1st atom in gro:     1MOL     C1    1   3.164   4.206
> 6.075
> The same thing was also found in a normal non-free energy simulations with
> combination of position restrain and refcoord-scaling.
> Later on, we found some other people also have the same problem when use
> that combination to do free energy calculation.
> http://comments.gmane.org/gmane.science.biology.gromacs.user/66177
> It makes more sense to me to turn on refcoord_scaling while using position
> restraint.
> Again, any help to understand this would be appreciated!
> Regards,
> Jin


Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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