Hi all:<br>I put three small molecules in the center of an POPC bilayer
membrane,and equilibriated this system in NPT ensemble for 10ns with the
position restriction of small molecules. Then I want to give each of
those molecules an external force to push them away from the center. the
force vecters are on the plane of membrane.<br>
I realize this using the SMD of Gromacs 4.5.3. But system was very unstable:<br>
When using pull=umbrella, after 1000~2000steps the small molecules in
the membrane was shifted along the X-axis or Y-axis very fast, <br>
When using pull=constraint,after 1000~2000steps the system was exploded, and serval atoms were shot out of system.<br>The mdp file of SMD is below:<br><br>pull_constr_tol = 1e-6<br>pull_geometry = direction<br>
pull_start = yes<br>pull_nstxout = 50<br>pull_nstfout = 50<br>pull_ngroups = 3<br>pull_group0 = ref ; the whole membrane which is on the plane of xy <br>pull_group1 = phe1 ; one of the small molecule<br>
pull_vec1 = -0.866 -0.5 0 <br>pull_rate1 = 0.001 ; [nm/ps] <br>pull_init1 = <br>pull_k1 = 1000 ; [kJ.mol-1.nm-2 / [kJ.mol-1.nm-1]] <br>
pull_group2 = phe2<br>pull_vec2 = 0 1 0 <div id=":yp"> <br>pull_rate2 = 0.001 ; [nm/ps] <br>pull_init2 = <br>
pull_k2 = 1000 ; [kJ.mol-1.nm-2 / [kJ.mol-1.nm-1]] <br>pull_group3 = phe3 <br>pull_vec3 = 0.866 -0.5 0 <br>pull_rate3 = 0.001 ; [nm/ps]<br>
pull_init3 = <br>pull_k3 = 1000 ; [kJ.mol-1.nm-2 / [kJ.mol-1.nm-1]]<br><br>and the time step: dt = 0.001 ; 1 fs<br> <br>Is there anyone could give me an suggestion for this?<br>
Thank you very much!<br><br><br>Yorquant Wang<br></div>