<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
<HTML><HEAD>
<META http-equiv=Content-Type content="text/html; charset=utf-8">
<META content="MSHTML 6.00.2800.1589" name=GENERATOR>
<STYLE></STYLE>
</HEAD>
<BODY bgColor=#ffffff>
<DIV><FONT face=幼圆 color=#008000>Hi <FONT
color=#000000>Wassenaar:</FONT></FONT></DIV>
<DIV><FONT face=幼圆 color=#008000></FONT> </DIV>
<DIV><FONT face=幼圆 color=#008000>As mensioned in GMX manual3.3 , the parameter
of OPLS force field is listed bellow:</FONT></DIV>
<DIV><FONT face=幼圆 color=#008000></FONT> </DIV>
<DIV><FONT face=幼圆
color=#008000>Name FUNCTION</FONT></DIV>
<DIV><FONT face=幼圆
color=#008000>bond
1</FONT></DIV>
<DIV><FONT face=幼圆
color=#008000>pair
1</FONT></DIV>
<DIV><FONT face=幼圆
color=#008000>angle
1</FONT></DIV>
<DIV><FONT face=幼圆
color=#008000>dihedral 3
</FONT></DIV>
<DIV><FONT face=幼圆
color=#008000>nb
1</FONT></DIV>
<DIV><FONT face=幼圆
color=#008000>Col 3</FONT></DIV>
<DIV><FONT face=幼圆 color=#008000></FONT> </DIV>
<DIV><FONT face=幼圆 color=#008000>In the manual,4.6.3 Treatment of Cutoffs,it is
said that "In the neighbor list all<BR>interaction pairs that fall within rlist
are stored. Furthermore, the interactions between pairs<BR>that do not fall
within rlist but do fall within max(rcoulomb,rvdw) are computed during<BR>NS,
and the forces and energy are stored separately, and added to short-range forces
at every time<BR>step between successive NS."</FONT></DIV>
<DIV><FONT face=幼圆 color=#008000></FONT> </DIV>
<DIV><FONT face=幼圆 color=#008000>From the paragraph, I concluded that when the
distance of cutoff is increased, the further interaction pair will be
considered. So the presion will be increased also.</FONT></DIV>
<DIV><FONT face=幼圆 color=#008000></FONT> </DIV>
<DIV><FONT face=幼圆 color=#008000>I modified the cutoff from 1.5 nm to 1.2
nm.Till now the system is not exploding. Whatever 1.5 nm or 1.2 nm, it has been
proved that 0.9 nm is too short to simulating with OPLS.</FONT></DIV>
<DIV><FONT face=幼圆 color=#008000></FONT> </DIV>
<DIV><FONT face=幼圆 color=#008000>By the way, where do you find the critical
value 1.2 nm. I can not found it by google. But there is really a lot of works
used that values. Thank you very much.</FONT></DIV>
<DIV><FONT face=幼圆 color=#008000></FONT> </DIV>
<DIV><FONT face=幼圆 color=#008000>For the IE format, these mail was copied from
WORD. Because I'm not confident with my English.:)</FONT></DIV>
<DIV><FONT face=幼圆 color=#008000></FONT> </DIV>
<DIV><FONT face=幼圆 color=#008000></FONT> </DIV>
<DIV>Message: 7<BR>Date: Fri, 9 Mar 2007 10:07:47 +0100<BR>From: "Tsjerk
Wassenaar" <<A
href="mailto:tsjerkw@gmail.com">tsjerkw@gmail.com</A>><BR>Subject: Re: Re:
[gmx-users] vacuum right but melt collapse<BR>To: "kitty ji" <<A
href="mailto:jiqing@iccas.ac.cn">jiqing@iccas.ac.cn</A>>, "Discussion list
for GROMACS<BR>users" <<A
href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</A>><BR>Message-ID:<BR><<A
href="mailto:8ff898150703090107i264e57cdt4ba6647115d284e3@mail.gmail.com">8ff898150703090107i264e57cdt4ba6647115d284e3@mail.gmail.com</A>><BR>Content-Type:
text/plain; charset=ISO-8859-1; format=flowed<BR><BR>Hi Kitty,<BR><BR>OPLS was
developed (IIRC) for use with a cut-off of 1.2 nm. Not<BR>shorter, not longer.
If you set the cut-off higher, you introduce<BR>additional force components;
noise, artefacts, not precision. It may<BR>be good to do some reading about
force fields and the parameterization<BR>thereof.<BR><BR>The reaction field is a
correction for the neglect of electrostatic<BR>interaction beyond the cut off.
It should be used when using a GROMOS<BR>force field, as those are parameterized
for use with it. Regarding<BR>OPLS, I'm not sure. I thought it was not
parameterized for use with<BR>RF, but either a plain cut-off or a cut-off with a
switch function.<BR>You should check the OPLS papers to be sure.<BR><BR>By the
way, please keep discussions on the list... In that way, it is<BR>publicly
archived, which potentially saves us a lot of trouble<BR>answering the same
questions over and over.<BR><BR>Cheers,<BR><BR>Tsjerk<BR><BR>On 3/9/07, kitty ji
<<A href="mailto:jiqing@iccas.ac.cn">jiqing@iccas.ac.cn</A>>
wrote:<BR>> Thanks for your reply.<BR>><BR>> The force field I used
here is OPLS. Increasing the cutoff means to increase the precision of
caluculation not "underlying cause". Therefore it is acceptable. In addition, it
is said that cutoff 9 angstrom is not enough for electricity
calculation.<BR>><BR>> what is using reaction-field? I thought it was not
used here.<BR>><BR>><BR>> ----- Original Message -----<BR>> From:
"Tsjerk Wassenaar" <<A
href="mailto:tsjerkw@gmail.com">tsjerkw@gmail.com</A>><BR>> To: "kitty ji"
<<A href="mailto:jiqing@iccas.ac.cn">jiqing@iccas.ac.cn</A>>; "Discussion
list for GROMACS users" <<A
href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</A>><BR>> Sent:
Thursday, March 08, 2007 10:34 PM<BR>> Subject: Re: Re: [gmx-users] vacuum
right but melt collapse<BR>><BR>><BR>> Hi Kitty,<BR>><BR>> Such a
solution is unsatisfactory, as it seems that you're masking an<BR>>
underlying cause. Now, I'm not sure of your other parameters, but when<BR>>
using a cut-off (do you use reaction-field) you would usually (gromos<BR>>
force field) use a twin-range of 0.9/1.4, which is what the force<BR>> field
was parameterized for.<BR>><BR>> If you look at the energies in order to
find the cause of a crash, you<BR>> want to look for the energy term first
displaying strange behaviour.<BR>> You also may want to try setting the
neighbour list update to every<BR>> step.<BR>><BR>> And please, don't
use html formatted e-mails... :)<BR>><BR>> Hope it helps,<BR>><BR>>
Tsjerk<BR>><BR>><BR>> On 3/8/07, kitty ji <<A
href="mailto:jiqing@iccas.ac.cn">jiqing@iccas.ac.cn</A>> wrote:<BR>>
><BR>> ><BR>> ><BR>> ><BR>> > Tsjerk Wassenaar, thank
you very much for you suggestion even if most of<BR>> > them have been
manipulated.<BR>> ><BR>> ><BR>> ><BR>> > "Write out the
energies at every step and check which of the energy<BR>> > contributions
goes astray. This may give you a good clue to where<BR>> > you're mistake
is. Also, run through the topology again, by hand,<BR>> > checking all
bonds, angles, dihedrals, exclusion (implicit ones!),<BR>> > etc."<BR>>
><BR>> > when the explosion happened, the energy of bond, angle and
potential will<BR>> > were increase. And the topology has been checked
several times.<BR>> ><BR>> ><BR>> ><BR>> ><BR>>
><BR>> > Now I increase the cutoff of VDW & Coulomb from 0.9 to
1.5. The system looks<BR>> > ok from last night to this time. If the
problem is fixed, I conclude that<BR>> > cutoff 0.9 is not enough for
electric system.<BR>> ><BR>> ><BR>> ><BR>> > Hope this
conclusion is helpful for GMX users.<BR>> ><BR>> ><BR>>
><BR>> > Message: 2<BR>> > Date: Wed, 7 Mar 2007 17:49:30
+0100<BR>> > From: "Tsjerk Wassenaar" <<A
href="mailto:tsjerkw@gmail.com">tsjerkw@gmail.com</A>><BR>> > Subject:
Re: Re: [gmx-users] vacuum right but melt collapse<BR>> > To: "kitty ji"
<<A href="mailto:jiqing@iccas.ac.cn">jiqing@iccas.ac.cn</A>>, "Discussion
list for GROMACS<BR>> > users" <<A
href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</A>><BR>> >
Message-ID:<BR>> > <<A
href="mailto:8ff898150703070849r59cb8a8dr60b894a881fcc331@mail.gmail.com">8ff898150703070849r59cb8a8dr60b894a881fcc331@mail.gmail.com</A>><BR>>
> Content-Type: text/plain; charset=GB2312; format=flowed<BR>>
><BR>> ><BR>> > Hi Ji Qing,<BR>> ><BR>> > Write out
the energies at every step and check which of the energy<BR>> >
contributions goes astray. This may give you a good clue to where<BR>> >
you're mistake is. Also, run through the topology again, by hand,<BR>> >
checking all bonds, angles, dihedrals, exclusion (implicit ones!),<BR>> >
etc.<BR>> ><BR>> > Good luck,<BR>> ><BR>> >
Tsjerk<BR>> ><BR>> > On 3/7/07, kitty ji <<A
href="mailto:jiqing@iccas.ac.cn">jiqing@iccas.ac.cn</A>> wrote:<BR>>
><BR>> > ><BR>> > ><BR>> > > Thanks Mark.<BR>>
> > But when one polymer chain was used, non-bonded interaction has
already<BR>> > been<BR>> > > there. Because one chain means
C44H156O22.<BR>> > > After all, I'd like to try more chains.<BR>>
> ><BR>> > > Message: 1<BR>> > > Date: Tue, 06 Mar 2007
17:01:52 +1100<BR>> > > From: Mark Abraham <<A
href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</A>><BR>>
><BR>> > > Subject: Re: [gmx-users] vacuum right but melt
collapse<BR>> > > To: Discussion list for GROMACS users <<A
href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</A>><BR>> >
> Message-ID: <<A
href="mailto:45ED03D0.6010803@anu.edu.au">45ED03D0.6010803@anu.edu.au</A>><BR>>
><BR>> > > Content-Type: text/plain; charset=GB2312<BR>> >
><BR>> > > kitty ji wrote:<BR>> > > > Hi GMX
user:<BR>> > > ><BR>> > > > A model for Poly(vinyl
methyl ether) was built with OPLS force field (<BR>> > > > all H
).<BR>> > > ><BR>> > > ><BR>> > > ><BR>>
> > > When the model was run alone (a single chain) in vacuum, anything
goes<BR>> > ok.<BR>> > > ><BR>> > > ><BR>> >
> ><BR>> > > > But with 45 chains box, the system will be
collapse with a little bond<BR>> > > > elongates abnormal whatever
in NVT or NPT.<BR>> > > ><BR>> > > ><BR>> > >
><BR>> > > > The relax time of pressure and temperature were
adjust but no helpful.<BR>> > > ><BR>> > > ><BR>>
> > ><BR>> > > > How can I found some possible reason and
then fix it ? Any advise will<BR>> > > > be appreciated.<BR>>
> ><BR>> > > If an isolated molecule doesn't do anything strange,
and two more more<BR>> > > do, then you have a problem with
inter-molecular interactions, i.e. the<BR>> > > non-bonded ones. Try
with just 2 chains to verify this... and look<BR>> > > carefully at the
atom types and the non-bonded parameters for them.<BR>> > ><BR>>
> > Mark<BR>> > ><BR>> > ><BR>> > ><BR>>
> > *************************************************<BR>> > > Ji
Qing<BR>> > > Institute of Chemistry, Chinese Academy of
Sciences<BR>> > > Tel: 0086-10-62562894 £¬82618423<BR>> >
> *************************************************<BR>> > >
_______________________________________________<BR>> > > gmx-users
mailing list <A
href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</A><BR>>
><BR>> > > <A
href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</A><BR>>
> > Please don't post (un)subscribe requests to the list. Use the<BR>>
> > www interface or send it to <A
href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</A>.<BR>>
> > Can't post? Read<BR>> > > <A
href="http://www.gromacs.org/mailing_lists/users.php">http://www.gromacs.org/mailing_lists/users.php</A><BR>>
> ><BR>> ><BR>> ><BR>> > --<BR>> > Tsjerk A.
Wassenaar, Ph.D.<BR>> > Junior UD (post-doc)<BR>> > Biomolecular
NMR, Bijvoet Center<BR>> > Utrecht University<BR>> > Padualaan
8<BR>> > 3584 CH Utrecht<BR>> > The Netherlands<BR>> > P:
+31-30-2539931<BR>> > F: +31-30-2537623<BR>> ><BR>> >
_______________________________________________<BR>> > gmx-users mailing
list <A
href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</A><BR>> > <A
href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</A><BR>>
> Please don't post (un)subscribe requests to the list. Use the<BR>> >
www interface or send it to <A
href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</A>.<BR>>
> Can't post? Read<BR>> > <A
href="http://www.gromacs.org/mailing_lists/users.php">http://www.gromacs.org/mailing_lists/users.php</A><BR>>
><BR>><BR>><BR>> --<BR>> Tsjerk A. Wassenaar, Ph.D.<BR>>
Junior UD (post-doc)<BR>> Biomolecular NMR, Bijvoet Center<BR>> Utrecht
University<BR>> Padualaan 8<BR>> 3584 CH Utrecht<BR>> The
Netherlands<BR>> P: +31-30-2539931<BR>> F: +31-30-2537623<BR><BR><BR>--
<BR>Tsjerk A. Wassenaar, Ph.D.<BR>Junior UD (post-doc)<BR>Biomolecular NMR,
Bijvoet Center<BR>Utrecht University<BR>Padualaan 8<BR>3584 CH Utrecht<BR>The
Netherlands<BR>P: +31-30-2539931<BR>F:
+31-30-2537623<BR><BR><BR>------------------------------<BR><BR>_______________________________________________<BR>gmx-users
mailing list<BR><A
href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</A><BR><A
href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</A><BR><BR><BR>End
of gmx-users Digest, Vol 35, Issue
22<BR>*****************************************</DIV></BODY></HTML>