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On 11/11/2011 5:13 PM, LindaSong wrote:
<blockquote
cite="mid:3a283ce0.5bde.1339142ceb1.Coremail.wlsonglinda@gmail.com"
type="cite">
<div style="line-height: 1.7; color: rgb(0, 0, 0); font-size:
14px; font-family: arial;">Thank you very much for your reply,
Mark<br>
<br>
It is the topology problem. It seems I did it in a wrong way.
Now the topology goes like this: <br>
<span style="FONT-SIZE: 18px"> <span style="FONT-SIZE:
13px"> [ molecules ]<br>
; Compound #mols<br>
Protein_chain_A 1 <br>
Protein_chain_A2 1<br>
POPC 256</span></span><br>
This problem solved.<br>
<br>
But then comes a new one. When I did the g_membed, the system
blowed up after one iteration!<br>
I think I really shouldn't ignore the warning from the grompp.
However, as an inexper ienced user, I don't know how to improve
the mdp file. Can you give me any hint?<br>
</div>
</blockquote>
<br>
Use a text editor that writes plain text. Junk "&nbsp;"
throughout cannot help things. As before, reporting the actual text
of the warning is critical to working out what might be wrong.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:3a283ce0.5bde.1339142ceb1.Coremail.wlsonglinda@gmail.com"
type="cite">
<div
style="line-height:1.7;color:#000000;font-size:14px;font-family:arial">The
mdp file for the g_membed is like this:<br>
<blockquote><span style="font-size: 13px;">cpp
= /lib/cpp</span><br>
<span style="font-size: 13px;">; Run parameters</span><br>
<span style="font-size: 13px;">integrator = md
</span><br>
<span style="font-size: 13px;">nsteps = 1000
</span><br>
<span style="font-size: 13px;">dt = 0.002
</span><br>
<span style="font-size: 13px;">; Output control</span><br>
<span style="font-size: 13px;">nstxout = 10&n
bsp; </span><br>
<span style="font-size: 13px;">nstvout = 10
</span><br>
<span style="font-size: 13px;">nstenergy = 10 </span><br>
<span style="font-size: 13px;">nstlog = 10
</span><br>
<span style="font-size: 13px;">; Bond parameters</span><br>
<span style="font-size: 13px;">continuation = no </span><br>
<span style="font-size: 13px;">constraint_algorithm = lincs
</span><br>
<span style="font-size: 13px;">constraints = all-bonds
</span><br>
<span style="font-size: 13px;">lincs_iter = 1 </span><br>
<span style="font-size: 13px;">lincs_order = 4
</span><br>
<span style="font-size: 13px;">; Neighborsearching</span><br>
<span style="font-size: 13px;">ns_type = grid </span><br>
<span style="font-size: 13px;">nstlist = 1
</span><br>
<span style="font-size: 13px;">rlist = 1.4
</span><br>
<span style="font-size: 13px;">rcoulomb = 1.4 </span><br>
<span style="font-size: 13px;">rvdw &nb sp; =
1.4 </span><br>
<span style="font-size: 13px;">; Electrostatics</span><br>
<span style="font-size: 13px;">coulombtype = PME </span><br>
<span style="font-size: 13px;">pme_order = 4 </span><br>
<span style="font-size: 13px;">fourierspacing = 0.16 </span><br>
<span style="font-size: 13px;">; Temperature coupling is on</span><br>
<span style="font-size: 13px;">tcoupl = V-rescale
</span><br>
<span style="font-size: 13px;">tc-grps = Protein
Non-Protein </span><br>
<span style="font-size: 13px;">tau_t = 0.1
0.1 & nbsp; </span><br>
<span style="font-size: 13px;">ref_t = 300 300
</span><br>
<span style="font-size: 13px;">; Pressure coupling is on</span><br>
<span style="font-size: 13px;">Pcoupl =
Berendsen</span><br>
<span style="font-size: 13px;">pcoupltype =
semiisotropic</span><br>
<span style="font-size: 13px;">tau_p = 1.0</span><br>
<span style="font-size: 13px;">compressibility =
4.5e-5 4.5e-5</span><br>
<span style="font-size: 13px;">ref_p ; =
1.0 1.0</span><br>
<span style="font-size: 13px;">; Velocity generation</span><br>
<span style="font-size: 13px;">gen_vel = yes</span><br>
<span style="font-size: 13px;">gen_temp = 300</span><br>
<span style="font-size: 13px;">gen_seed =
173529</span><br>
<span style="font-size: 13px;">; Energy monitoring</span><br>
<span style="font-size: 13px;">energygrps = Protein</span><br>
<span style="font-size: 13px;">; Non-equilibrium MD</span><br>
<span style="font-size: 13px;">freezegrps = Protein</span><br>
<span style="font-size: 13px;">freezedim &nb sp;
= Y Y Y</span><br>
<span style="font-size: 13px;">; Energy group exclusions</span><br>
<span style="font-size: 13px;">energygrp_excl = Protein
Protein</span><br>
</blockquote>
<br>
Thanks a lot!<br>
Linda<br>
<br>
<br>
<br>
</div>
<br>
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