[gmx-users] Freeze + NPT + constraints

[Justin Lemkul]

On 9/10/13 2:59 PM, HANNIBAL LECTER wrote:
> Hi,
>
> Sorry to bother you again regarding this. But I am not sure, as to why
> freeze + constraints should not work during a NPT simulation?
>
> The update algorithm as shown in the manual does not say anything that
> would fundamentally prevent this. In fact, one can use freezegroups +
> constraints in NVT. What prevents it from running in NPT?
>

The use of a barostat requires that the positions of the atoms can be scaled 
according to the pressure.  Freezing atoms, by definition, makes them immobile 
and thus they cannot be scaled.  Thus, the two algorithms are fundamentally 
incompatible.

-Justin

> I get the foll. error.
>
> step 0
> Step 1  Warning: pressure scaling more than 1%, mu: -2.7758e+23 -2.7758e+23
> -2.7758e+23
>
> Step 1  Warning: pressure scaling more than 1%, mu: -2.7758e+23 -2.7758e+23
> -2.7758e+23
>
> Step 1  Warning: pressure scaling more than 1%, mu: -2.7758e+23 -2.7758e+23
> -2.7758e+23
>
> Step 1  Warning: pressure scaling more than 1%, mu: -2.7758e+23 -2.7758e+23
> -2.7758e+23
>
> Step 1  Warning: pressure scaling more than 1%, mu: -2.7758e+23 -2.7758e+23
> -2.7758e+23
>
> Step 1  Warning: pressure scaling more than 1%, mu: -2.7758e+23 -2.7758e+23
> -2.7758e+23
>
> Step 1  Warning: pressure scaling more than 1%, mu: -2.7758e+23 -2.7758e+23
> -2.7758e+23
>
> Step 1  Warning: pressure scaling more than 1%, mu: -2.7758e+23 -2.7758e+23
> -2.7758e+23
> Warning: Triclinic box is too skewed.
> Warning: Triclinic box is too skewed.
> Warning: Triclinic box is too skewed.
> ...
> ...
> ...
> Segmentation fault
>

-- 
==================================================

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

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

==================================================