<br>Dear Gromacs Users,<br><br>I have been trying to simulate a protein in
implicit solvent. When I used a single processor by setting -nt to 1 , I
did not encounter any problem. But when I tried to run the simulations
using more than 1 processor I get the following error.<br>
<br>Fatal error:<br>Constraint dependencies further away than next-neighbor<br>in particle decomposition. Constraint between atoms 2177--2179 evaluated<br>on node 3 and 3, but atom 2177 has connections within 4 bonds (lincs_order)<br>
of node 1, and atom 2179 has connections within 4 bonds of node 3.<br>Reduce the # nodes, lincs_order, or<br>try domain decomposition.<br><br> I set the lincs_order parameter in .mdp file to different values. But it did not help. <br>
I have some questions regarding the information above.<br><br> 1) Is it possible to run implicit solvent simulations in parallel?<br><br> 2)
As far as I know gromacs uses domain decomposition as default. Why does in
my simulations gromacs use the particle decomposition which I do not
ask for.<br>
<br>Any suggestions are appreciated very much. <br> I am ussing
gromacs-4.5.4 with charmm force field and the OBC implicit solvent
model. If you need further informations, probably a run input file, let
me know.<br><br>Regards,<br><font color="#888888"><font color="#888888">
<br>Ozlem Ulucan</font></font>