<html><head><style type="text/css"><!-- DIV {margin:0px;} --></style></head><body><div style="font-family:times new roman, new york, times, serif;font-size:12pt"><DIV>Hi All,</DIV>
<DIV> In general what we do in pulling simulations that we pull one selection keeping the other fixed. In that case the distance between the two selections increases with time. Now, I want to push the selections i.e. one selection will be kept fixed and the other will be pushed towards the fixed one so that the distance between the two selection will decrease. Is it possible to do that in GROMACS? What should I modify in the mdp file? I am attaching a mdp file that I have used for pulling simulations (only the pull part).</DIV>
<DIV> </DIV>
<DIV>; pull code</DIV>
<DIV>pull = umbrella</DIV>
<DIV>pull_geometry = distance</DIV>
<DIV>pull_dim = N N Y</DIV>
<DIV>pull_start = yes</DIV>
<DIV>pull_ngroups = 1</DIV>
<DIV>pull_group0 = freeze</DIV>
<DIV>pull_group1 = pull</DIV>
<DIV>pull_rate1 = 0.01</DIV>
<DIV>pull_k1 = 1000</DIV>
<DIV> </DIV>
<DIV>I have used pull_dim N N Y as I am interested to pull only in the z direction. Should I just use N N -Y to do the compressing simulations? </DIV>
<DIV> </DIV>
<DIV>Please suggest.</DIV>
<DIV> </DIV>
<DIV>Thanks in advance.</DIV>
<DIV> </DIV>
<DIV>Samrat</DIV>
<DIV> </DIV></div><br>
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