Dear Justin.<br><br>Thank you for you answer.<br><br>But, the case I wrote, it was an ideally case. To help anyone in the forum at the same time.<br><br>As soon as I have read your answer I tried. In my case my simulations were:<br>
<br>First simulation: 0.4ns<br>Second : 1ns<br>Third: 2ns<br>Fourth: 10ns<br>----------------------<br>Total = 13.4ns<br><br>So I planned to do an RMSD plot of 0-13.4ns. As I said before, each simulation is the continuation of the previous, obviously to do this I used checkpoint files for each simulation and the same MD.mdp, only changed the time of simulation.<br>
<br>I did:<br><br>trajcat -f md_0_4ns_noPBC.xtc md_1ns_noPBC.xtc md_2ns_noPBC.xtc md_10ns_noPBC.xtc -o TOTAL_13_4ns_noPBC.xtc<br><br>Then for curiosity I did > ls -lh<br><br>rw-r--r-- 1 willy bioinfo 368M 2011-06-01 13:10 md_0_4_noPBC.xtc<br>
-rw-r--r-- 1 willy bioinfo 917M 2011-06-01 13:12 md_1ns_noPBC.xtc<br>-rw-r--r-- 1 willy bioinfo 917M 2011-06-01 13:13 md_2ns_noPBC.xtc<br>-rw-r--r-- 1 willy bioinfo 9.0G 2011-06-01 13:17 md_10ns_noPDB.xtc<br>
-rw-r--r-- 1 willy bioinfo 9.0G 2011-06-01 15:44 TOTAL_13_4ns_noPBC.xtc<br>
<br>Surprisingly the file "TOTAL_13_4ns_noPBC.xtc" had the same size of the file "md_10ns_noPDB.xtc", is it normal?<br><br>Continue with the process, then:<br><br>>g_rms -s molecule_sol_ion_MD_0_4ns.tpr -f TOTAL_13_4ns_noPDB.xtc -o rmsd_13_4ns_molecule.xvg -tu ns<br>
<br>I open the .XVG as a simple .txt and I noticed that the time only reach 10ns or 10000ps. Why not 13.4ns?<br><br>I would be very grateful If you can tell me what is happening.<br><br>Thanks in adavance.<br><br>Miguel Quiliano.<br>
<br><br><br><br><br><br><br><br><br><br><br><div class="gmail_quote">2011/6/1 <span dir="ltr"><<a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>></span><br><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
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Today's Topics:<br>
<br>
1. Re: scaling non-bonded interactions (Da-Wei Li)<br>
2. question about trajcat command: Merge files (Miguel Quiliano Meza)<br>
3. Re: Re: scaling non-bonded interactions (Justin A. Lemkul)<br>
4. Re: scaling non-bonded interactions (Justin A. Lemkul)<br>
5. Re: question about trajcat command: Merge files (Justin A. Lemkul)<br>
6. RE: Re: scaling non-bonded interactions (Kukol, Andreas)<br>
<br>
<br>
----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Wed, 1 Jun 2011 15:32:07 -0400<br>
From: Da-Wei Li <<a href="mailto:lidawei@gmail.com">lidawei@gmail.com</a>><br>
Subject: Re: [gmx-users] scaling non-bonded interactions<br>
To: <a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>, Discussion list for GROMACS users<br>
<<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID: <BANLkTinww3_rE7x-SyffAPY=<a href="mailto:RWPyxt2-5A@mail.gmail.com">RWPyxt2-5A@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
I remember that 1-4 won't be scaled in the free energy code, right?<br>
<br>
dawei<br>
<br>
On Wed, Jun 1, 2011 at 3:24 PM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>> wrote:<br>
<br>
><br>
><br>
> Kukol, Andreas wrote:<br>
><br>
>> Hello,<br>
>> Is it possible to globally scale all non-bonded interactions by a factor ?<br>
>> I know there are energy exclusion groups, but that is an all or nothing<br>
>> approach, while I would like to reduce non-bonded interaction potentials to<br>
>> e.g. 10% of their normal value.<br>
>><br>
>> If this is not possible, I suggest to have this as an option in the<br>
>> mdp-file.<br>
>><br>
>><br>
> You can do this with the free energy code.<br>
><br>
> couple-moltype = system<br>
> init_lambda = 0.9<br>
> couple_lambda0 = vdw-q<br>
> couple_lambda1 = none<br>
><br>
> Please note, though, that such settings will result in massive performance<br>
> loss, even for small systems. There is an open issue on the redmine server<br>
> about this, but no resolution yet.<br>
><br>
> -Justin<br>
><br>
> --<br>
> ========================================<br>
><br>
> Justin A. Lemkul<br>
> Ph.D. Candidate<br>
> ICTAS Doctoral Scholar<br>
> MILES-IGERT Trainee<br>
> Department of Biochemistry<br>
> Virginia Tech<br>
> Blacksburg, VA<br>
> jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
> <a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
><br>
> ========================================<br>
> --<br>
> gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
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Message: 2<br>
Date: Wed, 1 Jun 2011 15:34:49 -0400<br>
From: Miguel Quiliano Meza <<a href="mailto:rifaximina@gmail.com">rifaximina@gmail.com</a>><br>
Subject: [gmx-users] question about trajcat command: Merge files<br>
To: <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
Message-ID: <BANLkTi=<a href="mailto:ai0noWVV_g3Evvxxuqb1kCdAmTA@mail.gmail.com">ai0noWVV_g3Evvxxuqb1kCdAmTA@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="iso-8859-1"<br>
<br>
Dear community,<br>
<br>
I have a couple of doubts, please help me to clarify.<br>
<br>
I performed 4 MD simulations using Gromacs (each one of 1ns, 2ns, 3ns ,4ns)<br>
, they are only a continuation of the last, because of I was explored the<br>
rmsd variation along the time. Now I want to merge all the trajectories to<br>
do only one plot of 10ns.<br>
<br>
So, I did:<br>
<br>
trajcat -f md_1ns_noPBC.xtc md_2ns_noPBC.xtc md_3ns_noPBC.xtc<br>
md_4ns_noPBC.xtc -o TOTAL_10ns_noPBC.xtc<br>
<br>
The program showed this:<br>
<br>
File Start time Time step<br>
---------------------------------------------------------<br>
md_1ns_noPBC.xtc 0.000 ps 2.000 ps<br>
md_2ns_noPBC.xtc 0.000 ps 2.000 ps WARNING: same<br>
Start time as previous<br>
md_3ns_noPBC.xtc 0.000 ps 2.000 ps WARNING: same<br>
Start time as previous<br>
md_4ns_noPDB.xtc 0.000 ps 2.000 ps WARNING: same<br>
Start time as previous<br>
<br>
I am worry about the message 'WARNING: same Start time as previous', I think<br>
is normal because each simulation is like independent, that is the reason<br>
why start time is take as 0ps.<br>
<br>
Please tell me If my command line is correct according to my purposes. By<br>
the way, to make the plot (RMSD 10ns) I plan to do it with -s md_1ns.tpr, is<br>
it correct?<br>
<br>
Thank you in advance.<br>
<br>
Miguel Quiliano.<br>
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Message: 3<br>
Date: Wed, 01 Jun 2011 15:35:34 -0400<br>
From: "Justin A. Lemkul" <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>><br>
Subject: Re: [gmx-users] Re: scaling non-bonded interactions<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:4DE69486.5070203@vt.edu">4DE69486.5070203@vt.edu</a>><br>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed<br>
<br>
<br>
<br>
Vitaly Chaban wrote:<br>
> Doesn't increased temperature work for this purpose?<br>
><br>
><br>
<br>
REMD can be useful, yes, but generalized Hamiltonian exchange, using lambda to<br>
scale the interactions between molecules can be very effective, as well.<br>
<br>
-Justin<br>
<br>
><br>
> On Wed, Jun 1, 2011 at 3:27 PM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>> wrote:<br>
>><br>
>> Vitaly Chaban wrote:<br>
>>>> Is it possible to globally scale all non-bonded interactions by a factor<br>
>>>> ? I know there are energy exclusion groups, but that is an all or nothing<br>
>>>> approach, while I would like to reduce non-bonded interaction potentials to<br>
>>>> e.g. 10% of their normal value.<br>
>>>><br>
>>>> If this is not possible, I suggest to have this as an option in the<br>
>>>> mdp-file.<br>
>>><br>
>>> I don't see much sense in such uniform scaling.<br>
>>><br>
>>><br>
>> Such scaling can be useful for overcoming energy barriers and speeding up<br>
>> equilibration. This function is hinted at in the description of the<br>
>> couple-moltype .mdp keyword. I don't know if that's the intent here, but it<br>
>> certainly does have an application.<br>
>><br>
>> -Justin<br>
>><br>
>> --<br>
>> ========================================<br>
>><br>
>> Justin A. Lemkul<br>
>> Ph.D. Candidate<br>
>> ICTAS Doctoral Scholar<br>
>> MILES-IGERT Trainee<br>
>> Department of Biochemistry<br>
>> Virginia Tech<br>
>> Blacksburg, VA<br>
>> jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
>> <a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
>><br>
>> ========================================<br>
>><br>
><br>
><br>
><br>
<br>
--<br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
========================================<br>
<br>
<br>
------------------------------<br>
<br>
Message: 4<br>
Date: Wed, 01 Jun 2011 15:38:17 -0400<br>
From: "Justin A. Lemkul" <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>><br>
Subject: Re: [gmx-users] scaling non-bonded interactions<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:4DE69529.6000801@vt.edu">4DE69529.6000801@vt.edu</a>><br>
Content-Type: text/plain; charset=UTF-8; format=flowed<br>
<br>
<br>
<br>
Da-Wei Li wrote:<br>
> I remember that 1-4 won't be scaled in the free energy code, right?<br>
><br>
<br>
True, but the desired 10% scaling in this case can be applied by changing the<br>
FudgeLJ and FudgeQQ values of the force field, I believe.<br>
<br>
-Justin<br>
<br>
> dawei<br>
><br>
> On Wed, Jun 1, 2011 at 3:24 PM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a><br>
> <mailto:<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>>> wrote:<br>
><br>
><br>
><br>
> Kukol, Andreas wrote:<br>
><br>
> Hello,<br>
> Is it possible to globally scale all non-bonded interactions by<br>
> a factor ? I know there are energy exclusion groups, but that<br>
> is an all or nothing approach, while I would like to reduce<br>
> non-bonded interaction potentials to e.g. 10% of their normal value.<br>
><br>
> If this is not possible, I suggest to have this as an option in<br>
> the mdp-file.<br>
><br>
><br>
> You can do this with the free energy code.<br>
><br>
> couple-moltype = system<br>
> init_lambda = 0.9<br>
> couple_lambda0 = vdw-q<br>
> couple_lambda1 = none<br>
><br>
> Please note, though, that such settings will result in massive<br>
> performance loss, even for small systems. There is an open issue on<br>
> the redmine server about this, but no resolution yet.<br>
><br>
> -Justin<br>
><br>
> --<br>
> ========================================<br>
><br>
> Justin A. Lemkul<br>
> Ph.D. Candidate<br>
> ICTAS Doctoral Scholar<br>
> MILES-IGERT Trainee<br>
> Department of Biochemistry<br>
> Virginia Tech<br>
> Blacksburg, VA<br>
> jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> <<a href="http://vt.edu" target="_blank">http://vt.edu</a>> | (540) 231-9080<br>
> <tel:%28540%29%20231-9080><br>
> <a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
><br>
> ========================================<br>
> --<br>
> gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
> <mailto:<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
> <a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
> Please search the archive at<br>
> <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br>
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><br>
><br>
<br>
--<br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
========================================<br>
<br>
<br>
------------------------------<br>
<br>
Message: 5<br>
Date: Wed, 01 Jun 2011 15:40:45 -0400<br>
From: "Justin A. Lemkul" <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>><br>
Subject: Re: [gmx-users] question about trajcat command: Merge files<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:4DE695BD.7030304@vt.edu">4DE695BD.7030304@vt.edu</a>><br>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed<br>
<br>
<br>
<br>
Miguel Quiliano Meza wrote:<br>
> Dear community,<br>
><br>
> I have a couple of doubts, please help me to clarify.<br>
><br>
> I performed 4 MD simulations using Gromacs (each one of 1ns, 2ns, 3ns<br>
> ,4ns) , they are only a continuation of the last, because of I was<br>
> explored the rmsd variation along the time. Now I want to merge all the<br>
> trajectories to do only one plot of 10ns.<br>
><br>
> So, I did:<br>
><br>
> trajcat -f md_1ns_noPBC.xtc md_2ns_noPBC.xtc md_3ns_noPBC.xtc<br>
> md_4ns_noPBC.xtc -o TOTAL_10ns_noPBC.xtc<br>
><br>
> The program showed this:<br>
><br>
> File Start time Time step<br>
> ---------------------------------------------------------<br>
> md_1ns_noPBC.xtc 0.000 ps 2.000 ps<br>
> md_2ns_noPBC.xtc 0.000 ps 2.000 ps WARNING: same<br>
> Start time as previous<br>
> md_3ns_noPBC.xtc 0.000 ps 2.000 ps WARNING: same<br>
> Start time as previous<br>
> md_4ns_noPDB.xtc 0.000 ps 2.000 ps WARNING: same<br>
> Start time as previous<br>
><br>
> I am worry about the message 'WARNING: same Start time as previous', I<br>
> think is normal because each simulation is like independent, that is the<br>
> reason why start time is take as 0ps.<br>
><br>
<br>
This may be correct for your case (if in the .mdp file you have "tinit = 0") or<br>
you otherwise did not properly continue the simulation using a checkpoint file.<br>
If it makes sense to concatenate independent trajectories and consider them to<br>
be continuous, you can override the start times with the -settime option.<br>
<br>
> Please tell me If my command line is correct according to my purposes.<br>
> By the way, to make the plot (RMSD 10ns) I plan to do it with -s<br>
> md_1ns.tpr, is it correct?<br>
><br>
<br>
That will calculate RMSD relative to the structure contained in the .tpr file<br>
that began the first 1-ns simulation. If that's what you wish to measure, then<br>
you're correct.<br>
<br>
-Justin<br>
<br>
--<br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
========================================<br>
<br>
<br>
------------------------------<br>
<br>
Message: 6<br>
Date: Wed, 1 Jun 2011 20:34:46 +0100<br>
From: "Kukol, Andreas" <<a href="mailto:a.kukol@herts.ac.uk">a.kukol@herts.ac.uk</a>><br>
Subject: RE: [gmx-users] Re: scaling non-bonded interactions<br>
To: "<a href="mailto:vvchaban@gmail.com">vvchaban@gmail.com</a>" <<a href="mailto:vvchaban@gmail.com">vvchaban@gmail.com</a>>, Discussion list for<br>
GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID:<br>
<<a href="mailto:2F848DC922C8D741BF3A60B7D7108B6A9EF2AC3578@UH-MAILSTOR.herts.ac.uk">2F848DC922C8D741BF3A60B7D7108B6A9EF2AC3578@UH-MAILSTOR.herts.ac.uk</a>><br>
Content-Type: text/plain; charset="us-ascii"<br>
<br>
I want to use it to energy minimise a system that has severe clashes. The EM always crashes, even if I reduce the step-size. It could also be useful for NMR refinement to allow atoms to move through each other in order to satisfy distance restraints.<br>
<br>
Andreas<br>
________________________________________<br>
From: <a href="mailto:gmx-users-bounces@gromacs.org">gmx-users-bounces@gromacs.org</a> [<a href="mailto:gmx-users-bounces@gromacs.org">gmx-users-bounces@gromacs.org</a>] On Behalf Of Vitaly Chaban [<a href="mailto:vvchaban@gmail.com">vvchaban@gmail.com</a>]<br>
Sent: 01 June 2011 20:30<br>
To: <a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a><br>
Cc: <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
Subject: Re: [gmx-users] Re: scaling non-bonded interactions<br>
<br>
Doesn't increased temperature work for this purpose?<br>
<br>
<br>
<br>
On Wed, Jun 1, 2011 at 3:27 PM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>> wrote:<br>
><br>
><br>
> Vitaly Chaban wrote:<br>
>>><br>
>>> Is it possible to globally scale all non-bonded interactions by a factor<br>
>>> ? I know there are energy exclusion groups, but that is an all or nothing<br>
>>> approach, while I would like to reduce non-bonded interaction potentials to<br>
>>> e.g. 10% of their normal value.<br>
>>><br>
>>> If this is not possible, I suggest to have this as an option in the<br>
>>> mdp-file.<br>
>><br>
>><br>
>> I don't see much sense in such uniform scaling.<br>
>><br>
>><br>
><br>
> Such scaling can be useful for overcoming energy barriers and speeding up<br>
> equilibration. This function is hinted at in the description of the<br>
> couple-moltype .mdp keyword. I don't know if that's the intent here, but it<br>
> certainly does have an application.<br>
><br>
> -Justin<br>
><br>
> --<br>
> ========================================<br>
><br>
> Justin A. Lemkul<br>
> Ph.D. Candidate<br>
> ICTAS Doctoral Scholar<br>
> MILES-IGERT Trainee<br>
> Department of Biochemistry<br>
> Virginia Tech<br>
> Blacksburg, VA<br>
> jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
> <a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
><br>
> ========================================<br>
><br>
<br>
<br>
<br>
--<br>
Dr. Vitaly V. Chaban, Department of Chemistry<br>
University of Rochester, Rochester, New York 14627-0216<br>
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