[gmx-users] Re: gmx-users Digest, Vol 59, Issue 1
drugdesign
drugdesign at yandex.ru
Sun Mar 1 07:04:13 CET 2009
Mark, thank you very much for the answer. I can't find this issue in the archives. If it's not difficult to you, won't you be so kind to send the link on it.
Best regards,
Andrew
01.03.09, 08:14, gmx-users-request at gromacs.org:
> Send gmx-users mailing list submissions to
> gmx-users at gromacs.org
> To subscribe or unsubscribe via the World Wide Web, visit
> http://www.gromacs.org/mailman/listinfo/gmx-users
> or, via email, send a message with subject or body 'help' to
> gmx-users-request at gromacs.org
> You can reach the person managing the list at
> gmx-users-owner at gromacs.org
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of gmx-users digest..."
> Today's Topics:
> 1. Re: atomtype OWT4 not found but OWT3 and OWT5 is ok in
> amber03 force field....how is that possible? (Mark Abraham)
> 2. RE: Cannot obtain the expected pressure using the
> Parrinello-Rahman coupling in a gas-liquid system (GuoGuangjun)
> ----------------------------------------------------------------------
> Message: 1
> Date: Sun, 01 Mar 2009 10:08:50 +1100
> From: Mark Abraham <Mark.Abraham at anu.edu.au>
> Subject: Re: [gmx-users] atomtype OWT4 not found but OWT3 and OWT5 is
> ok in amber03 force field....how is that possible?
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <49A9C402.2030600 at anu.edu.au>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> drugdesign wrote:
> > I am trying to use amber03 force field for GROMACS with TIP4P water molecules. But I've got an error about OWT4 atom type.
> > The strange is that with TIP3P and TIP5P it works ok. Some time ago it worked ok with TIP4P too...maybe I've changed sometheing but now I get the log listed below...
> > How is that possible?
> > -------------------------------------------------------
> > Program grompp, VERSION 4.0.2
> > Source code file: toppush.c, line: 897
> >
> > Fatal error:
> > Atomtype OWT4 not found
> > -------------------------------------------------------
> IIRC, there was some issue with an early GROMACS 4.0.x and TIP4P. Search
> the archives for more information. To solve, I suggest you update.
> Mark
> ------------------------------
> Message: 2
> Date: Sun, 1 Mar 2009 05:09:39 +0000
> From: GuoGuangjun <guogj at hotmail.com>
> Subject: RE: [gmx-users] Cannot obtain the expected pressure using the
> Parrinello-Rahman coupling in a gas-liquid system
> To: Gromacs-BBS <gmx-users at gromacs.org>
> Message-ID: <COL101-W62FB2B80795C1D1F68B528BFA80 at phx.gbl>
> Content-Type: text/plain; charset="gb2312"
> Hi,
> After I recheck the box, it is indeed the case described in bugzilla 165. The length of box increases in the Z-direction and decreases in the X/Y-direction with time. When I prolong the run, it exits abnormally at the time when the Box-X/Y reduces to a value less than 2*rvdw. When I fix the Box-Z by setting the compressibility as zero, the semiisotropic with P-R barostat produces the inaccurate pressure again. Now, I have to use the Berendsen barostat for my methane-water interface system.
> Guang-Jun
>
> > Date: Sat, 28 Feb 2009 19:53:10 +0100
> > From: spoel at xray.bmc.uu.se
> > To: gmx-users at gromacs.org
> > Subject: Re: [gmx-users] Cannot obtain the expected pressure using the Parrinello-Rahman coupling in a gas-liquid system
> >
> > GuoGuangjun wrote:
> > > Hi,
> > >
> > >
> > > The question is resolved by changing the pcoupltype from isotropic to
> > > semiisotropic. Correspondingly, the compressibility and ref_p are given
> > > for the x/y and z directions with the same original values,
> > > respectively. The test system includes 300 methane, 1725 water, and 300
> > > methane, forming two interfaces parallel to the xy-plane. Now, the
> > > accurate average-total-pressure is obtained from a short run (0.2 ns)
> > > with the default tau_p (1 ps).
> >
> > Please be careful when you use this kind of pressure coupling, you may
> > get the right pressure but you box might keep growing in one direction
> > forever. See bugzilla 165. Actually I'm pretty sure it will.
> > Unfortunately we don't really understand what is going on here.
> > >
> > >
> > >
> > > Thank you for your kind replies and useful clues.
> > >
> > > Guang-Jun
> > >
> > > ------------------------------------------------------------------------
> > > From: gmx3 at hotmail.com
> > > To: gmx-users at gromacs.org
> > > Subject: RE: [gmx-users] Cannot obtain the expected pressure using the
> > > Parrinello-Rahman coupling in a gas-liquid system
> > > Date: Sat, 28 Feb 2009 15:00:50 +0100
> > >
> > > Hi,
> > >
> > > Is 327 bar the averge total pressure or one the of components of the
> > > pressure tensor?
> > > You will have a surface tension acting in the system causing a
> > > difference in the different components.
> > >
> > > Also it is still not completely clear to me how long you equilibrate and
> > > average.
> > > Also the results will depend very much on the size of the system.
> > > In small systems the pressure fluctuations are enormous.
> > > With Berendsen these fluctuations will be surpressed, with PR not.
> > >
> > > With PR I would use a tau_p of around 10 ps.
> > > You might need to average the pressure over several (tens of?) ns (after
> > > several ns of equilibration)
> > > to obtain a good average.
> > >
> > > Berk
> > >
> > > ------------------------------------------------------------------------
> > > From: guogj at hotmail.com
> > > To: gmx-users at gromacs.org
> > > Subject: RE: [gmx-users] Cannot obtain the expected pressure using the
> > > Parrinello-Rahman coupling in a gas-liquid system
> > > Date: Sat, 28 Feb 2009 13:51:15 +0000
> > >
> > > Hi, Justin,
> > >
> > > Thanks for your rapid reply. Let me decribes the question in more details.
> > > First ,two gaseous mathane systems and one liquid water system are
> > > equilibrated at 300 bar and 250 K in advance. Then, the gas systems are
> > > put at the both sides of liquid. The combined system is performed for
> > > 3ns with the Parrinello-Rahman barostat, which produces a average
> > > pressure of 327 bar. I am strange to the value and several tests are
> > > run, mentioned previously. All these test runs take the end gro file of
> > > the 3ns-run as the beginning. When the berendsen barostat is used,
> > > the pressure is OK. When the Parrinello-Rahman barostat is used, the
> > > questionary pressure occurs again. Although I will try to make a long
> > > run for equilibrium, I think the equilibrium has reached because the
> > > ~330 bar is always obtained no matter how long simulations are sampled,
> > > from 0.2 ns to 3 ns. The version of Gromacs I used is 4.0.4. By the way,
> > > how long did you equilibrate your membrane system and how many atoms
> > > in it? Thanks again.
> > >
> > > Guang-Jun
> > >
> > >
> > >
> > > > Date: Sat, 28 Feb 2009 07:43:29 -0500
> > > > From: jalemkul at vt.edu
> > > > To: gmx-users at gromacs.org
> > > > Subject: Re: [gmx-users] Cannot obtain the expected pressure using
> > > the Parrinello-Rahman coupling in a gas-liquid system
> > > >
> > > >
> > > >
> > > > GuoGuangjun wrote:
> > > > > In fact, I once run the gas-liquid interface for 3 ns, the pressure is
> > > > > still as high as 327 bar.
> > > >
> > > > There are two possibilities in my mind:
> > > >
> > > > 1. 3 ns is still not long enough.
> > > > 2. Your gas phase is causing the problem. If the pressure is right
> > > for water
> > > > alone, then the problem likely comes from the inclusion of your gas
> > > phase and
> > > > whatever parameters you're using for whatever species you have in
> > > this phase.
> > > > Examine your parameters and consider how they were derived and
> > > whether or not
> > > > they are adequate.
> > > >
> > > > Also, what version of Gromacs are you using? There were some changes
> > > made to
> > > > the Parrinello-Rahman barostat between 3.3.x and 4.0.x.
> > > >
> > > > -Justin
> > > >
> > > > > Guang-Jun
> > > > >
> > > > >
> > > > > > Date: Sat, 28 Feb 2009 07:19:30 -0500
> > > > > > From: jalemkul at vt.edu
> > > > > > To: gmx-users at gromacs.org
> > > > > > Subject: Re: [gmx-users] Cannot obtain the expected pressure using
> > > > > the Parrinello-Rahman coupling in a gas-liquid system
> > > > > >
> > > > > >
> > > > > >
> > > > > > GuoGuangjun wrote:
> > > > > > >
> > > > > > > Hi, All,
> > > > > > > I am simulating an interface system composed of methane gas and
> > > liquid
> > > > > > > water in the NPT ensemble. The temperature is well controlled
> > > by using
> > > > > > > either the Berendsen or the Nose-Hoover T-couplings. As for
> > > pressure,
> > > > > > > the Berendsen P-coupling also works well. However, the
> > > > > Parrinello-Rahman
> > > > > > > P-coupling always produces a higher pressure than the expected. For
> > > > > > > example, I set ref_p=300 bar in the mdp file but obtain an average
> > > > > > > pressure as ~330 bar (over 0.5 ns). I test the tau_p in the range
> > > > > 0.1 ~
> > > > > > > 10 ps, the case does not change. When I test the sin! ! gle-phase
> > > > > system,
> > > > > > > i.e., pure water, the Parrinello-Rahman P-coupling can indeed
> > > produce
> > > > > > > the expected pressure with the deviation less than 2 bar. What
> > > is the
> > > > > > > matter in the two-phase system?
> > > > > > >
> > > > > >
> > > > > > When I've used the Parrinello-Rahman barostat for membrane systems,
> > > > > it works
> > > > > > just fine. Perhaps 500 ps is too short of a timeframe to arrive at
> > > > > the average.
> > > > > > Heterogeneous systems often take longer to equilibrate.
> > > > > >
> > > > > > -Justin
> > > > > >
> > > > > > > Thanks a lot.
> > > > > > > Guang-Jun
> > > > > > >
> > > > > > >
> > > > >
> > > ------------------------------------------------------------------------
> > > > > > > ������ MSN ���� MSN ��� ���������
> > > > > > > <http://im.live.cn/safe/>
> > > > > > >
> > > > > > >
> > > > > > >
> > > > >
> > > ------------------------------------------------------------------------
> > > > > > >
> > > > > > > _______________________________________________
> > > > > > >! ! ; gmx-users mailing list gmx-users at gromacs.org
> > > > > > > http://www.gromacs.org/mailman/listinfo/gmx-users
> > > > > > > Please search the archive at http://www.gromacs.org/search before
> > > > > posting!
> > > > > > > Please don't post (un)subscribe requests to the list. Use the
> > > > > > > www interface or send it to gmx-users-request at gromacs.org.
> > > > > > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> > > > > >
> > > > > > --
> > > > > > ========================================
> > > > > >
> > > > > > Justin A. Lemkul
> > > > > > Graduate Research Assistant
> > > > > > Department of Biochemistry
> > > > > > Virginia Tech
> > > > > > Blacksburg, VA
> > > > > > jalemkul[at]vt.edu | (540) 231-9080
> > > > > > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> > > > > >
> > > > > > ========================================
> > > > > > _______________________________________________
> > > > > > gmx-users mailing list gmx-users at gromacs.org
> > > > > > http://www.gromacs.org/mailman/listinfo/gmx-users
> > > > > > Please! ! search the archive at http://www.gromacs.org/search before
> > > > > posting!
> > > > > > Please don't post (un)subscribe requests to the list. Use the
> > > > > > www interface or send it to gmx-users-request at gromacs.org.
> > > > > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> > > > >
> > > > >
> > > ------------------------------------------------------------------------
> > > > > �������������θ������������������� �ȩ�
> > > > > <http://ditu.live.com/?form=MICHAJ >
> > > >
> > > > --
> > > > ========================================
> > > >
> > > > Justin A. Lemkul
> > > > Graduate Research Assistant
> > > > Department of Biochemistry
> > > > Virginia Tech
> > > > Blacksburg, VA
> > > > jalemkul[at]vt.edu | (540) 231-9080
> > > > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> > > >
> > > > ========================================
> > > > _______________________________________________
> > > > gmx-users mailing list gmx-users at gromacs.org
> > > > http://www.gromacs.org/mailman/listinfo/gmx-users
> > > > Please search the archive at http://www.gromacs.org/search before
> > > posting!
> > > > Please don't post (un)subscribe requests to the list. Use the
> > > > www interface or send it to gmx-users-request at gromacs.org.
> > > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> > >
> > > ------------------------------------------------------------------------
> > > �������������θ������������������� �ȩ�
> > > <http://ditu.live.com/?form=MICHAJ>
> > > ------------------------------------------------------------------------
> > > Express yourself instantly with MSN Messenger! MSN Messenger
> > > <http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/>
> > > ------------------------------------------------------------------------
> > > MSN 9.0 �������������25G������� ������
> > > <http://im.live.cn/msn9/>
> > >
> > >
> > > ------------------------------------------------------------------------
> > >
> > > _______________________________________________
> > > gmx-users mailing list gmx-users at gromacs.org
> > > http://www.gromacs.org/mailman/listinfo/gmx-users
> > > Please search the archive at http://www.gromacs.org/search before posting!
> > > Please don't post (un)subscribe requests to the list. Use the
> > > www interface or send it to gmx-users-request at gromacs.org.
> > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> >
> >
> > --
> > David van der Spoel, Ph.D., Professor of Biology
> > Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
> > Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
> > spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
> > _______________________________________________
> > gmx-users mailing list gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at http://www.gromacs.org/search before posting!
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-request at gromacs.org.
> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> _________________________________________________________________
> ��Windows Live ��������������� MSN�
> http://im.live.cn/
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL: http://www.gromacs.org/pipermail/gmx-users/attachments/20090301/7be264a4/attachment.html
> ------------------------------
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> End of gmx-users Digest, Vol 59, Issue 1
> ****************************************
> Send gmx-users mailing list submissions to
> gmx-users at gromacs.org
> To subscribe or unsubscribe via the World Wide Web, visit
> http://www.gromacs.org/mailman/listinfo/gmx-users
> or, via email, send a message with subject or body 'help' to
> gmx-users-request at gromacs.org
> You can reach the person managing the list at
> gmx-users-owner at gromacs.org
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of gmx-users digest..."
> Today's Topics:
> 1. Re: atomtype OWT4 not found but OWT3 and OWT5 is ok in
> amber03 force field....how is that possible? (Mark Abraham)
> 2. RE: Cannot obtain the expected pressure using the
> Parrinello-Rahman coupling in a gas-liquid system (GuoGuangjun)
> ----------------------------------------------------------------------
> Message: 1
> Date: Sun, 01 Mar 2009 10:08:50 +1100
> From: Mark Abraham <Mark.Abraham at anu.edu.au>
> Subject: Re: [gmx-users] atomtype OWT4 not found but OWT3 and OWT5 is
> ok in amber03 force field....how is that possible?
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <49A9C402.2030600 at anu.edu.au>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> drugdesign wrote:
> > I am trying to use amber03 force field for GROMACS with TIP4P water molecules. But I've got an error about OWT4 atom type.
> > The strange is that with TIP3P and TIP5P it works ok. Some time ago it worked ok with TIP4P too...maybe I've changed sometheing but now I get the log listed below...
> > How is that possible?
> > -------------------------------------------------------
> > Program grompp, VERSION 4.0.2
> > Source code file: toppush.c, line: 897
> >
> > Fatal error:
> > Atomtype OWT4 not found
> > -------------------------------------------------------
> IIRC, there was some issue with an early GROMACS 4.0.x and TIP4P. Search
> the archives for more information. To solve, I suggest you update.
> Mark
> ------------------------------
> Message: 2
> Date: Sun, 1 Mar 2009 05:09:39 +0000
> From: GuoGuangjun <guogj at hotmail.com>
> Subject: RE: [gmx-users] Cannot obtain the expected pressure using the
> Parrinello-Rahman coupling in a gas-liquid system
> To: Gromacs-BBS <gmx-users at gromacs.org>
> Message-ID: <COL101-W62FB2B80795C1D1F68B528BFA80 at phx.gbl>
> Content-Type: text/plain; charset="gb2312"
> Hi,
> After I recheck the box, it is indeed the case described in bugzilla 165. The length of box increases in the Z-direction and decreases in the X/Y-direction with time. When I prolong the run, it exits abnormally at the time when the Box-X/Y reduces to a value less than 2*rvdw. When I fix the Box-Z by setting the compressibility as zero, the semiisotropic with P-R barostat produces the inaccurate pressure again. Now, I have to use the Berendsen barostat for my methane-water interface system.
> Guang-Jun
>
> > Date: Sat, 28 Feb 2009 19:53:10 +0100
> > From: spoel at xray.bmc.uu.se
> > To: gmx-users at gromacs.org
> > Subject: Re: [gmx-users] Cannot obtain the expected pressure using the Parrinello-Rahman coupling in a gas-liquid system
> >
> > GuoGuangjun wrote:
> > > Hi,
> > >
> > >
> > > The question is resolved by changing the pcoupltype from isotropic to
> > > semiisotropic. Correspondingly, the compressibility and ref_p are given
> > > for the x/y and z directions with the same original values,
> > > respectively. The test system includes 300 methane, 1725 water, and 300
> > > methane, forming two interfaces parallel to the xy-plane. Now, the
> > > accurate average-total-pressure is obtained from a short run (0.2 ns)
> > > with the default tau_p (1 ps).
> >
> > Please be careful when you use this kind of pressure coupling, you may
> > get the right pressure but you box might keep growing in one direction
> > forever. See bugzilla 165. Actually I'm pretty sure it will.
> > Unfortunately we don't really understand what is going on here.
> > >
> > >
> > >
> > > Thank you for your kind replies and useful clues.
> > >
> > > Guang-Jun
> > >
> > > ------------------------------------------------------------------------
> > > From: gmx3 at hotmail.com
> > > To: gmx-users at gromacs.org
> > > Subject: RE: [gmx-users] Cannot obtain the expected pressure using the
> > > Parrinello-Rahman coupling in a gas-liquid system
> > > Date: Sat, 28 Feb 2009 15:00:50 +0100
> > >
> > > Hi,
> > >
> > > Is 327 bar the averge total pressure or one the of components of the
> > > pressure tensor?
> > > You will have a surface tension acting in the system causing a
> > > difference in the different components.
> > >
> > > Also it is still not completely clear to me how long you equilibrate and
> > > average.
> > > Also the results will depend very much on the size of the system.
> > > In small systems the pressure fluctuations are enormous.
> > > With Berendsen these fluctuations will be surpressed, with PR not.
> > >
> > > With PR I would use a tau_p of around 10 ps.
> > > You might need to average the pressure over several (tens of?) ns (after
> > > several ns of equilibration)
> > > to obtain a good average.
> > >
> > > Berk
> > >
> > > ------------------------------------------------------------------------
> > > From: guogj at hotmail.com
> > > To: gmx-users at gromacs.org
> > > Subject: RE: [gmx-users] Cannot obtain the expected pressure using the
> > > Parrinello-Rahman coupling in a gas-liquid system
> > > Date: Sat, 28 Feb 2009 13:51:15 +0000
> > >
> > > Hi, Justin,
> > >
> > > Thanks for your rapid reply. Let me decribes the question in more details.
> > > First ,two gaseous mathane systems and one liquid water system are
> > > equilibrated at 300 bar and 250 K in advance. Then, the gas systems are
> > > put at the both sides of liquid. The combined system is performed for
> > > 3ns with the Parrinello-Rahman barostat, which produces a average
> > > pressure of 327 bar. I am strange to the value and several tests are
> > > run, mentioned previously. All these test runs take the end gro file of
> > > the 3ns-run as the beginning. When the berendsen barostat is used,
> > > the pressure is OK. When the Parrinello-Rahman barostat is used, the
> > > questionary pressure occurs again. Although I will try to make a long
> > > run for equilibrium, I think the equilibrium has reached because the
> > > ~330 bar is always obtained no matter how long simulations are sampled,
> > > from 0.2 ns to 3 ns. The version of Gromacs I used is 4.0.4. By the way,
> > > how long did you equilibrate your membrane system and how many atoms
> > > in it? Thanks again.
> > >
> > > Guang-Jun
> > >
> > >
> > >
> > > > Date: Sat, 28 Feb 2009 07:43:29 -0500
> > > > From: jalemkul at vt.edu
> > > > To: gmx-users at gromacs.org
> > > > Subject: Re: [gmx-users] Cannot obtain the expected pressure using
> > > the Parrinello-Rahman coupling in a gas-liquid system
> > > >
> > > >
> > > >
> > > > GuoGuangjun wrote:
> > > > > In fact, I once run the gas-liquid interface for 3 ns, the pressure is
> > > > > still as high as 327 bar.
> > > >
> > > > There are two possibilities in my mind:
> > > >
> > > > 1. 3 ns is still not long enough.
> > > > 2. Your gas phase is causing the problem. If the pressure is right
> > > for water
> > > > alone, then the problem likely comes from the inclusion of your gas
> > > phase and
> > > > whatever parameters you're using for whatever species you have in
> > > this phase.
> > > > Examine your parameters and consider how they were derived and
> > > whether or not
> > > > they are adequate.
> > > >
> > > > Also, what version of Gromacs are you using? There were some changes
> > > made to
> > > > the Parrinello-Rahman barostat between 3.3.x and 4.0.x.
> > > >
> > > > -Justin
> > > >
> > > > > Guang-Jun
> > > > >
> > > > >
> > > > > > Date: Sat, 28 Feb 2009 07:19:30 -0500
> > > > > > From: jalemkul at vt.edu
> > > > > > To: gmx-users at gromacs.org
> > > > > > Subject: Re: [gmx-users] Cannot obtain the expected pressure using
> > > > > the Parrinello-Rahman coupling in a gas-liquid system
> > > > > >
> > > > > >
> > > > > >
> > > > > > GuoGuangjun wrote:
> > > > > > >
> > > > > > > Hi, All,
> > > > > > > I am simulating an interface system composed of methane gas and
> > > liquid
> > > > > > > water in the NPT ensemble. The temperature is well controlled
> > > by using
> > > > > > > either the Berendsen or the Nose-Hoover T-couplings. As for
> > > pressure,
> > > > > > > the Berendsen P-coupling also works well. However, the
> > > > > Parrinello-Rahman
> > > > > > > P-coupling always produces a higher pressure than the expected. For
> > > > > > > example, I set ref_p=300 bar in the mdp file but obtain an average
> > > > > > > pressure as ~330 bar (over 0.5 ns). I test the tau_p in the range
> > > > > 0.1 ~
> > > > > > > 10 ps, the case does not change. When I test the sin! ! gle-phase
> > > > > system,
> > > > > > > i.e., pure water, the Parrinello-Rahman P-coupling can indeed
> > > produce
> > > > > > > the expected pressure with the deviation less than 2 bar. What
> > > is the
> > > > > > > matter in the two-phase system?
> > > > > > >
> > > > > >
> > > > > > When I've used the Parrinello-Rahman barostat for membrane systems,
> > > > > it works
> > > > > > just fine. Perhaps 500 ps is too short of a timeframe to arrive at
> > > > > the average.
> > > > > > Heterogeneous systems often take longer to equilibrate.
> > > > > >
> > > > > > -Justin
> > > > > >
> > > > > > > Thanks a lot.
> > > > > > > Guang-Jun
> > > > > > >
> > > > > > >
> > > > >
> > > ------------------------------------------------------------------------
> > > > > > > Ю╘КНАРЭ MSN ╦Щ╦╦СН MSN УМУ╦ НФРГЛНАРЭ╦
> > > > > > > <http://im.live.cn/safe/>
> > > > > > >
> > > > > > >
> > > > > > >
> > > > >
> > > ------------------------------------------------------------------------
> > > > > > >
> > > > > > > _______________________________________________
> > > > > > >! ! ; gmx-users mailing list gmx-users at gromacs.org
> > > > > > > http://www.gromacs.org/mailman/listinfo/gmx-users
> > > > > > > Please search the archive at http://www.gromacs.org/search before
> > > > > posting!
> > > > > > > Please don't post (un)subscribe requests to the list. Use the
> > > > > > > www interface or send it to gmx-users-request at gromacs.org.
> > > > > > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> > > > > >
> > > > > > --
> > > > > > ========================================
> > > > > >
> > > > > > Justin A. Lemkul
> > > > > > Graduate Research Assistant
> > > > > > Department of Biochemistry
> > > > > > Virginia Tech
> > > > > > Blacksburg, VA
> > > > > > jalemkul[at]vt.edu | (540) 231-9080
> > > > > > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> > > > > >
> > > > > > ========================================
> > > > > > _______________________________________________
> > > > > > gmx-users mailing list gmx-users at gromacs.org
> > > > > > http://www.gromacs.org/mailman/listinfo/gmx-users
> > > > > > Please! ! search the archive at http://www.gromacs.org/search before
> > > > > posting!
> > > > > > Please don't post (un)subscribe requests to the list. Use the
> > > > > > www interface or send it to gmx-users-request at gromacs.org.
> > > > > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> > > > >
> > > > >
> > > ------------------------------------------------------------------------
> > > > > ДжЛДжДУЙУыДДЧн╦╘╘кЧМУлЭЛПТотФТДЭЛХ╦ Юх╘╦
> > > > > <http://ditu.live.com/?form=MICHAJ >
> > > >
> > > > --
> > > > ========================================
> > > >
> > > > Justin A. Lemkul
> > > > Graduate Research Assistant
> > > > Department of Biochemistry
> > > > Virginia Tech
> > > > Blacksburg, VA
> > > > jalemkul[at]vt.edu | (540) 231-9080
> > > > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> > > >
> > > > ========================================
> > > > _______________________________________________
> > > > gmx-users mailing list gmx-users at gromacs.org
> > > > http://www.gromacs.org/mailman/listinfo/gmx-users
> > > > Please search the archive at http://www.gromacs.org/search before
> > > posting!
> > > > Please don't post (un)subscribe requests to the list. Use the
> > > > www interface or send it to gmx-users-request at gromacs.org.
> > > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> > >
> > > ------------------------------------------------------------------------
> > > ДжЛДжДУЙУыДДЧн╦╘╘кЧМУлЭЛПТотФТДЭЛХ╦ Юх╘╦
> > > <http://ditu.live.com/?form=MICHAJ>
> > > ------------------------------------------------------------------------
> > > Express yourself instantly with MSN Messenger! MSN Messenger
> > > <http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/>
> > > ------------------------------------------------------------------------
> > > MSN 9.0 СыИтХННЗ╦ЧяЖаЪ25GЛэАцЯЕК╦ Ю╘КНАРЭ╦
> > > <http://im.live.cn/msn9/>
> > >
> > >
> > > ------------------------------------------------------------------------
> > >
> > > _______________________________________________
> > > gmx-users mailing list gmx-users at gromacs.org
> > > http://www.gromacs.org/mailman/listinfo/gmx-users
> > > Please search the archive at http://www.gromacs.org/search before posting!
> > > Please don't post (un)subscribe requests to the list. Use the
> > > www interface or send it to gmx-users-request at gromacs.org.
> > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> >
> >
> > --
> > David van der Spoel, Ph.D., Professor of Biology
> > Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
> > Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
> > spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
> > _______________________________________________
> > gmx-users mailing list gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at http://www.gromacs.org/search before posting!
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-request at gromacs.org.
> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> _________________________________________________________________
> ХНWindows Live ФОгИБП╗╦НАРЭБмОАт MSN╦
> http://im.live.cn/
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL: http://www.gromacs.org/pipermail/gmx-users/attachments/20090301/7be264a4/attachment.html
> ------------------------------
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> End of gmx-users Digest, Vol 59, Issue 1
> ****************************************
More information about the gromacs.org_gmx-users
mailing list