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<DIV><FONT face=Arial size=2> <FONT face="Times New Roman" size=3>Dear GMX
users,</FONT></FONT></DIV>
<DIV>I am simulating the hydrophobic interaction between two 42-aminoacid
oligopeptides in pbc conditions with acqueous explicit solvent
with all-bonds constraints (LINCS). </DIV>
<DIV>In order to allow them to interact -for the first time- I am using
pull code.</DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2><FONT face="Times New Roman" size=3>My pull.ppa is
as follows</FONT></DIV>
<DIV><FONT size=3></FONT> </DIV>
<DIV><FONT face="Courier New" size=3>verbose = no</FONT></DIV>
<DIV><FONT face="Courier New" size=3></FONT><FONT face="Courier New"
size=3>runtype = afm</FONT></DIV>
<DIV><FONT face="Courier New" size=3></FONT><FONT face="Courier New"
size=3>group_1 = protein_2</FONT></DIV>
<DIV><FONT face="Courier New" size=3></FONT><FONT face="Courier New"
size=3>reference_group = protein_1</FONT></DIV>
<DIV><FONT face="Courier New" size=3></FONT><FONT face="Courier New"
size=3>reftype = com_t0</FONT></DIV>
<DIV><FONT face="Courier New" size=3></FONT><FONT face="Courier New"
size=3>reflag = 1</FONT></DIV>
<DIV><FONT face="Courier New" size=3></FONT><FONT face="Courier New"
size=3>pulldim = Y Y Y</FONT></DIV>
<DIV><FONT size=3></FONT> </DIV>
<DIV><FONT face=Arial size=3><FONT face="Times New Roman">Supposing that in my
sistem the two proteins (interacting groups) are distant 50 nm at time 0 and I
would like to cover this distance in about 2000 ps.</FONT></FONT></DIV>
<DIV><FONT face=Arial size=3><FONT face="Times New Roman">Should I use
an</FONT></FONT></DIV>
<DIV><FONT face="Times New Roman" size=3></FONT> </DIV>
<DIV><FONT face="Courier New" size=3>afm_rate1 = 0.025 (50ns/2000ps)<FONT
face="Times New Roman">?</FONT></FONT></DIV>
<DIV><FONT size=3></FONT> </DIV>
<DIV><FONT size=3></FONT> </DIV>
<DIV><FONT face="Times New Roman" size=3>Can anyone suggest
me the force constant value to simulate the hydrophobic
interaction (<FONT face="Courier New">afm_k1</FONT>) ?</FONT></DIV>
<DIV><FONT face="Times New Roman"><FONT size=3>How can I set the unit
vector describing the direction of pulling (<FONT
face="Courier New">afm_dir1</FONT>) ?</FONT></DIV></FONT>
<DIV align=left><FONT face="Times New Roman" size=3></FONT> </DIV>
<DIV align=left><FONT face=Arial size=3><FONT face="Times New Roman">May I set
the initial position relative to the reference group as</FONT></FONT></DIV>
<DIV><FONT size=3></FONT> </DIV>
<DIV><FONT size=3><FONT face="Courier New">afm_init1 = 0 0 0</FONT></FONT></DIV>
<DIV><FONT size=3></FONT> </DIV>
<DIV><FONT size=3></FONT> </DIV>
<DIV><FONT face="Times New Roman" size=3>I am using GROMACS 3.2.1, does pull
code work in parallel?</FONT></DIV>
<DIV><FONT face="Times New Roman" size=3></FONT> </DIV>
<DIV><FONT face="Times New Roman" size=3>Sorry for the long message and I hope
someone would help me.</FONT></DIV>
<DIV><FONT face="Times New Roman" size=3>Thanks in advance.</FONT></DIV>
<DIV><FONT face="Times New Roman" size=3></FONT> </DIV>
<DIV><FONT face="Times New Roman" size=3>Marino</FONT></DIV></FONT>
<DIV><FONT face=Arial><FONT size=2><FONT face=Arial
size=2></FONT></FONT></FONT> </DIV>
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size=2></FONT></FONT></FONT> </DIV>
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size=2></FONT></FONT></FONT> </DIV>
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size=2></FONT></FONT></FONT> </DIV>
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size=2></FONT></FONT></FONT> </DIV>
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