[gmx-users] Freeze + NPT + constraints

[HANNIBAL LECTER]

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.

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.
On Sep 10, 2013 4:12 PM, "Justin Lemkul" <jalemkul at 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 at outerbanks.umaryland.**edu <jalemkul at outerbanks.umaryland.edu> | (410)
> 706-7441
>
> ==============================**====================
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