From: Puspita Halder (puspitah_at_gmail.com)
Date: Fri Aug 31 2012 - 00:46:05 CDT
Hi Chris,
Thanks for your mail. I've heard about the term vacuum bubble , is this
totally devoid of any solvent molecule? I guess my situations is not
exactly so as I already mentioned that I've got a non-uniform water
distribution around the protein in the solvation box. Sorry, I didn't
measure the density of water molecules in the different region of the box
yet. I used some tcl scripts earlier but I am not so familiar with writing
such scripts. Do you have any script available what I can use for this type
of density calculation?
Thanks for your help.
Puspita
On Thu, Aug 30, 2012 at 6:45 PM, Puspita Halder <puspitah_at_gmail.com>
>
> 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--e89a8f6474fdd6d85b04c8894e95--
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