From: Akshay Bhatnagar (akshaybhatnagar2790_at_gmail.com)
Date: Tue Jun 03 2014 - 07:26:41 CDT
Thank you Ana
The point i wanted to mention is that the decrease in density is before
equilibration and minimization itself. but the information you gave is
useful, may be i should increase the box size. Actually i am simulating a
single amino acid i.e why i had chosen a 10 A box.
BITS Pilani Hyderabad Campus
On Tue, Jun 3, 2014 at 4:59 PM, Ana Celia Vila Verde <acavilaverde_at_gmail.com
> Dear Akshay,
> The reduction in volume that you see during equilibration is normal; after
> the equilibration the water will have the correct density, which is what
> you want. If you prefer a 10 A water cube, use solvate.tcl to create a 11
> A cube; after equilibration it should have an edge length close to 10 A.
> Keep in mind, though, that if your water cube has an edge that's 10 A then
> you need a cutoff for the non-bonded interactions of no more than 5 A.
> This will not work well because most water force-fields were parameterized
> with cutoff distances of order 9 to 12 A. This means that simulation boxes
> should not have edge lengths smaller than 18 to 24 A (twice the cutoff
> I hope this helps,
> On 03/06/14 12:22, Akshay Bhatnagar wrote:
>> I want to create a 10 A water cube but whenever i use the solvate.tcl
>> script to do the same the density of the box deceases due to which the same
>> of box is deformed in equilibration and production run.
>> can anyone help me please?
>> With Regards
>> Akshay Bhatnagar
>> PhD Student
>> BITS Pilani Hyderabad Campus
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