From: Puspita Halder (puspitah_at_gmail.com)
Date: Thu Aug 30 2012 - 08:15:51 CDT
Hi Norman,
Thanks for your mail. So your suggestion is to carry out the simulation at
300K under NPT condition since I started my run from one of the structures
taken from a 500K trajectroty under the same condition . I am little
confused here. Did you mean to say that running the simulation at 300K
under NPT followed by annealing under NVT or running that under NPT as a
whole?
I didn't get the point of different orientated water layers or hydrophobic
and hydrophilic effects. Can you clarify this a little more? I didn't
measure the water density exactly but by loading the trajectory in vmd it
seemed that water distribution around the protein is not uniform.
Thanks again.
Puspita
On Thu, Aug 30, 2012 at 1:26 PM, Norman Geist <
norman.geist_at_uni-greifswald.de> wrote:
> Also, ****
>
> ** **
>
> if the method you measure the density with, is really correct, couldn’t it
> be that your proteins hydrate shell is just like that because of different
> orientated water layers or hydrophobic and hydrophilic effects?****
>
> ** **
>
> Norman Geist.****
>
> ** **
>
> *Von:* Norman Geist [mailto:norman.geist_at_uni-greifswald.de]
> *Gesendet:* Donnerstag, 30. August 2012 08:50
> *An:* 'Puspita Halder'
> *Cc:* Namd Mailing List (namd-l_at_ks.uiuc.edu)
> *Betreff:* AW: namd-l: question regarding simulated annealing****
>
> ** **
>
> Hi,****
>
> ** **
>
> I could imagine that the NPT run with a temperature of 500K generates
> slightly other box dimensions as with 300K. So maybe you would have to NPT
> again under the 300K conditions.****
>
> ** **
>
> Norman Geist.****
>
> ** **
>
> *Von:* owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] *Im
> Auftrag von *Puspita Halder
> *Gesendet:* Dienstag, 28. August 2012 14:04
> *An:* namd-l_at_ks.uiuc.edu
> *Betreff:* namd-l: question regarding simulated annealing****
>
> ** **
>
> Dear NAMD users,
>
>
> I have a question regarding the water density in the solvation box during
> a simulated annealing run. I have started the simulated annealing run of my
> protein from a structure taken from a high temperature (500K) trajectory of
> the same generated after the minimization, heating and md run for ~2 ns at
> 500K temperature under NPT condiition. I decreased the temperature of my
> system staring from 500 K to 300 K in 5K temperature steps and for each and
> individual temperature step I equilibrated the system for 100 ps and
> finally equilibrated the system at 300K for 2 ns under NVT condition. The
> annealing run was seemed to be ok from the log file . The only problem that
> I found is the water density around the protein in the solvation box. This
> is found to be kind of inhomogeneous means in some portion of the box water
> is more dense whereas in the other portion it is less dense though the
> protein remains always solvated . Is this due to the effect of temperature
> decrease or something else? I have checked the xst file for the dimension
> of the box and it was fixed.
>
> If you need my config file for the simulated annealing run I'd send that.
>
> If anyone of you have any clue regarding this please let me know.
>
> Thanks for your help in advance.
>
> Puspita ****
>
>
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