On 9/10/13 5:17 PM, HANNIBAL LECTER wrote:
I would think that too. However, that is not what happens. If you freeze a
group it gets scaled according to the box vectors during a npt simulation.
Are the positions of the atoms actually changing? If they are, that's a bug.
It shouldn't happen, and in previous version of Gromacs, I know it didn't. Can
you point to the code that is making this happen?
Hence in order to keep the group (in my case a carbon nano tube) of fixed
diameter i use position restraints. This protocol works fine with with npt
simulations.
Now, i wanted to check if i include the bonded interactions in my topology
and constrain all the bonds things should not matter at all, since the
bonded interactions are redundant in this case. However, that is not the
case and the system crashes. If however the bonds are not constrained,
things work fine.
I know this is a very round about way of getting things done, still i am
curious.
Constraints and barostats both try to modify coordinates. The freezegrps
mechanism prevents modifications of coordinates, so what you're trying to
satisfy is a barostat that wants to scale coordinates (you say that is
accomplished somehow; I would like to see the evidence so the issue can be
addressed) and a constraint algorithm that wants to satisfy bond lengths. One
of those is bound to fail. I can imagine that if the initial configuration
perfectly satisfied the constraints, then maybe the run could proceed (because
freezegrps and constraints wouldn't be fighting one another), but I still can't
get my head around any way that you could satisfy freezing and a barostat.
In reality, what we should do is make it a fatal error, because truly, frozen
groups should be used very sparingly and certainly never with NPT. It just
doesn't make sense. I understand what you're trying to accomplish, but the
underlying theory becomes flawed.
-Justin
On Sep 10, 2013 4:12 PM, "Justin Lemkul" <jalem...@vt.edu> wrote:
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@outerbanks.umaryland.**edu <jalem...@outerbanks.umaryland.edu> | (410)
706-7441
==============================**====================
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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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