[gmx-users] Water residence time
feenstra at chem.vu.nl
Thu May 8 10:35:04 CEST 2003
> On Tue, 2003-05-06 at 19:10, Andrea Bernini wrote:
>>Dear gmx users,
>> I would like to compute residence time of water molecules on a protein
>>surface using a md trajectory of a solvated system. Is it possible to
>>carry out such calculation using Gromacs tools?
> Yes, check out g_hbond. You'll have to do it in two steps.
It will only look at hydrogen bonded waters.
>>If not, is it possible to obtain a list of water molecules that are
>>closer than a given distance to the protein for each frame?
> Yes, using trjorder
or g_mindist, using a cut-off distance it will give you the number of
residues (in this case, water molecules), within that distance to a
reference group (which would be your protein).
| | |
| _ _ ___,| K. Anton Feenstra |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|( | )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands |
| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610 |
| | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/ |
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