<div class="aju"><span class="gD">Tsjerk,<br><br><br>As Justin already has noticed there were lot of examples of implementation of the high temperature aproach to increase conformation sampling. This could be usefull because of short time-scale of typical MD trajectory and hight energy barriers of the adjacent energy-minimums wich could correspond to the functional-relevant conformations. So the main reason of such stimulations in to dicrease such barriers to promote transitions to the functional-relevant states conformations Finally I can sample the output of such simulation and compare this resulted conformations with the experimental data. If I obtain good similarity this may indicate about efficiency of such aproach<br>
<br>On other hand such simulation could result in some non-native conformations due to the non-native condtions. So the artificial restrains like as the distance restrains within native conformation ( obttained by NMR for instance) could be usefull-aproach to keep the system in the native-like conformations while enhansing sampling of the native-like structures via rising of temperatures. So combinations of such tricks could give physical-relevant results partly couldn't it ? However I suppose that the main disadvantage of such aproach is the non-physical intermediate states produced by non-native transitions pathways wich could arrise from such simulation. <br>
<br><br><br>James<br></span></div><br><div class="gmail_quote">11 апреля 2012 г. 18:09 пользователь Tsjerk Wassenaar <span dir="ltr"><<a href="mailto:tsjerkw@gmail.com">tsjerkw@gmail.com</a>></span> написал:<br><blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
Hey James,<br>
<br>
Have you thought about the physical relevance of your results?<br>
<br>
Cheers,<br>
<br>
Tsjerk<br>
<div class="HOEnZb"><div class="h5"><br>
On Wed, Apr 11, 2012 at 12:01 PM, James Starlight<br>
<<a href="mailto:jmsstarlight@gmail.com">jmsstarlight@gmail.com</a>> wrote:<br>
> Tsjerk,<br>
><br>
> Thank you for suggestions!<br>
><br>
><br>
> Indeed the hight temperature ( I'm using 700K) which I use for enhansing<br>
> sampling rate resulted in destabilisation of the secondary structure.<br>
><br>
> To prevent this I've used two slightly different aproaches based on the<br>
> restraint. But in both cases I've used slightly soft restrains with<br>
> fs=10-200.<br>
><br>
> The first aproach is the ussage of the posres applied on each backbone atom<br>
> with fc=10-50. I've tested case with fc=50 and found that such restrains<br>
> were very hight. I've not noticed any conformation sampling of my protein (<br>
> rmsd of backbone < 0.3 nm) during 10ns of such simulation. So I've decided<br>
> to test a case with fc=10 ( under calculation)<br>
><br>
> The second approach is the application of the harmonic distance restrainse<br>
> wich I've applied on each backbone atom pair in the CUTOFF radius of 1.0 nm.<br>
> The Rc value was chosen because of my protein is the 7 buddle of alpha<br>
> helices so this aproach could be usefull but exactly value for R have been<br>
> chosen empirically. I've selected deviation value wich are equal to 1\2 of<br>
> cutoff radius = 1.5 nm. I have not realise whaat I could obtain yet from<br>
> this because I'm not quite sure about coccect values of such disres.<br>
><br>
><br>
> James<br>
><br>
> 11 апреля 2012 г. 13:35 пользователь Tsjerk Wassenaar <<a href="mailto:tsjerkw@gmail.com">tsjerkw@gmail.com</a>><br>
> написал:<br>
>><br>
>> Hey :)<br>
>><br>
>> I'd say a protein should be loosing structure at 700K. Can't even say<br>
>> the force field is wrong there, even though it hasn't been<br>
>> parameterized for such temperatures for certain. You'd have to check<br>
>> with experiments.<br>
>> Trying to do high-temperature simulations is fine. But trying to do<br>
>> high temperature simulations to get results that match a room/body<br>
>> temperature ensemble is completely bogus. If you aim to use this<br>
>> approach for enhanced sampling, you're in for some serious<br>
>> reparameterization. Part of the deal may indeed be adding<br>
>> long(er)-range distance restraints. However, the force constants to<br>
>> use will increase with temperature, and with very high temperatures<br>
>> the force constants may end up so high that they give rise to fast<br>
>> oscillations, which will require using a smaller time step.<br>
>><br>
>> Just my 2 cents...<br>
>><br>
>> Tsjerk<br>
>><br>
>> --<br>
>> Tsjerk A. Wassenaar, Ph.D.<br>
>><br>
>> post-doctoral researcher<br>
>> Molecular Dynamics Group<br>
>> * Groningen Institute for Biomolecular Research and Biotechnology<br>
>> * Zernike Institute for Advanced Materials<br>
>> University of Groningen<br>
>> The Netherlands<br>
>> --<br>
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<br>
<br>
<br>
--<br>
Tsjerk A. Wassenaar, Ph.D.<br>
<br>
post-doctoral researcher<br>
Molecular Dynamics Group<br>
* Groningen Institute for Biomolecular Research and Biotechnology<br>
* Zernike Institute for Advanced Materials<br>
University of Groningen<br>
The Netherlands<br>
--<br>
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</div></div></blockquote></div><br>