Hello Andrea,<br><br>Thank you for your suggestion!<br><br>If my protein/membrane system has some clashes, how can I find them and correct them, cause I am not very clear when you say "removed them". I checked my starting structure with VMD many times, it seemed all right. Could you please give me some further suggestions?
<br><br>Thanks in advance!<br><br><div><span class="gmail_quote">On 12/15/05, <b class="gmail_sendername">andrea spitaleri</b> <<a href="mailto:spitaleri.andrea@hsr.it">spitaleri.andrea@hsr.it</a>> wrote:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hi<br>
I had a similar problem with protein/membrane system and I found that
the starting structure was wrong. Precisly, there were few clashes
between atoms of the protein with the membrane. Once removed them, the
min worked fine.<br>
I hope this can help,<br>
Regards<br>
<br>
Andrea<br>
<br>
liu xin wrote:
<blockquote cite="http://midc5eecdc0512150422y2def18e5j91d565e1f080e2e1@mail.gmail.com" type="cite"><div><span class="e" id="q_1082e6989b071632_1">Dear GROMACS users,<br>
<br>
My minizization problem still got no
resolvment, even I restarted from make hole, using different values for
"hfm", I got almost the same message when I try to minimize my
lipid/protein system. so I send this mail again asking for help. <br>
<br>
I checked the output energy, after SD minimization with my
lipid/protein system, found the values are abnormal:<br>
<br>
##########################################################################<br>
Steepest Descents converged to machine precision in 15 steps,<br>
but did not reach the requested Fmax < 2000.
<br>
Potential Energy = nan<br>
Maximum force = inf on atom 9614<br>
Norm of force = nan<br>
##########################################################################<br>
<br>
Then I checked the em.log line by line, found there are two message:<br>
<br>
##########################################################################<br>
Stepsize too small, or no change in energy.
<br>
Converged to machine precision,<br>
but not to the requested precision Fmax < 2000<br>
<br>
Double precision normally gives you higher accuracy.<br>
You might need to increase your constraint accuracy, or turn<br>
off constraints alltogether (set constraints = none in mdp file)
<br>
##########################################################################<br>
<br>
Infact I did set "constraints = none" in mdp file, and I got
the same result when changing the stepsize from 0.002 to 0.02. I
searched this forum, somebody said it is because of bad start
structure, so I restarted from makeing hole, using hfm = 5, 10, 10 then
100, 100, 150, but I still got almost the same result, except that the
atom number of "Maximum force" varies, I am new to
gromacs, I've been stuck into this problem for a week, could anybody
give me some suggestions? Any suggestions will
be highly appriciated!<br>
<br>
Thanks in advance!
</span></div><pre><hr size="4" width="90%">
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<br>
<div>-- <br>
-------------------------------<br>
Andrea Spitaleri <br>
Dulbecco Telethon Institute<br>
c/o DIBIT Scientific Institute<br>
Biomolecular NMR, 1B4<br>
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20132 Milano (Italy)<br>
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