[gmx-users] t_trxframe speed units

aherz alexander.herz at mytum.de
Fri Sep 4 10:05:27 CEST 2009


yes, I tried pull_start=yes (you also suggested trying constraint
instead of umbrella, which I tried as well).
my box is rectangular.


Berk Hess schrieb:
> Hi,
> The only thing I suggested was using pull_start=yes,
> otherwise you will start at a "random" distance and you will have enormous  forces.
> Did you try that?
> Do you have a rectangular or a triclinic box?
> Berk
>> Date: Thu, 3 Sep 2009 18:00:44 +0200
>> From: alexander.herz at mytum.de
>> To: gmx-users at gromacs.org
>> Subject: Re: [gmx-users] t_trxframe speed units
>> Hey,
>> I tried everything you suggested and a couple more things and still it
>> is not possible to get a reasonable speed
>> for the pulled groups (always way beyond the 0.01nm/ps set in the mdp
>> file and mostly containing some high frequence patttern probably related
>> to pbc). (I tried: constraint, pbcatoms, direction,position and using no
>> ref group).
>> Can I send you a small sample system with the problem or is there
>> something else I can do?
>> Thx,
>> Alex
>> Berk Hess schrieb:
>>> But you can not talk about popping back, since there is pbc.
>>> What matters is how the pull code determines the distance.
>>> At least in 4.0.4 and 4.0.5 it add the rate*t before doing pbc,
>>> such that it pulls smoothly even if the distance is larger than the box
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