[gmx-users] More than one settle type
mark.abraham at anu.edu.au
Wed Jan 26 05:45:14 CET 2011
On 01/26/11, Shalabh <shalabh at ufl.edu> wrote:
> I am trying to find the free energy of a water molecule as it adsorbs on a surface. My outline is:
> 1) Run the simulation
> 2) Analyze the results, find out which water molecule(s) are adsorbed
> 3) Create different groups for the water adsordbed molecule(s), create new .gro file (to identify the adsorbed water with different residue name), .mdp file and .tpe file. The remaining water molecules have the same previous group name.
You're making life hard for yourself by renaming the residue, which you don't need to do. You merely need to divide the solvent into two groups for energy evaluation, and you can do that with a suitably constructed index file and matching .mdp as grompp input. If you use g_select with a suitable geometric criterion for adsorbation, then it can write the index file for you (and there are various ways you might visualise the result to check it). All you need to do is decide on the criterion, name the groups, modify the .mdp and feed it to grompp.
> 4) Use mdrun -rerun to evaluate the energy between the new water group(s), the surface and the remaining water.
> When I try to implement this, I get an error in step 4 while running mdrun -rerun, saying "More than one settle type. Suggestion: change the least use settle constraints into 3 normal constraints". The .itp file which I created for the new water group is identical to the spc.itp file (with the only change as the residue name).
> This similar problem was raised earlier as well, which I am not sure if it was resolved:
> Basically, what I am trying to do is if I have 1000 water molecules in my system, can I have 999 of them in one group SOL, and the remaning 1 water molecule in a different group, say SOL1. The .itp files and parameters are identical, apart from the group (residue) name. And I am getting the above error. Anyone any ideas?
Groups and molecule blocks in the topology need not relate to each other at all. It is simplest to leave your .top file alone and follow the approach I suggested above.
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