[gmx-users] GMX 2018 and 'distance' pull
jalemkul at vt.edu
Tue Mar 13 17:27:54 CET 2018
On 3/13/18 10:32 AM, Alex wrote:
> It appears that things have improved... I am just glancing and pullf
> and pullx data from the first sample config and both contain only one
> value, even though we set dim to 3D. Does this make sense?
I haven't used the 2018 pull code yet. Presumably this is correct, just
the distance rather than all its components, though that would be a
change from previous versions.
> On 3/13/2018 8:18 AM, Justin Lemkul wrote:
>> On 3/13/18 10:17 AM, Alex wrote:
>>>>> You may have a situation that requires manual assignment of
>>>>> pull_group1_pbcatom1, as the automatic choice of
>>>> Sorry, that should be pull_group1_pbcatom. Must remind myself not
>>>> to email before coffee...
>>> Did you mean pull_group2_pbcatom? In my case:
>>> pull_group1_name = K
>>> pull_group2_name = CNT
>>> The language for 5.1 pull is (you be the judge on how clear it is):
>>> (0) The reference atom for the treatment of periodic boundary
>>> conditions inside the group (this has no effect on the treatment of
>>> the pbc between groups). This option is only important when the
>>> diameter of the pull group is larger than half the shortest box
>>> vector. For determining the COM, all atoms in the group are put at
>>> their periodic image which is closest topull-group1-pbcatom
>>> A value of 0 means that the middle atom (number wise) is used. This
>>> parameter is not used withpull-group1-geometrycylinder. A value of
>>> -1 turns on cosine weighting, which is useful for a group of
>>> molecules in a periodic system,/e.g./a water slab (see Engin et al.
>>> J. Chem. Phys. B 2010).
>>> Indeed, my group2 is a membrane that is wider than the shortest
>>> half-box. I am assuming it would be a single atom belonging to the
>>> pore region...
>> Yes, pull_group2_pbcatom, not 1.
Justin A. Lemkul, Ph.D.
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalemkul at vt.edu | (540) 231-3129
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