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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
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