Re: periodic cell has become too small for original patch grid

From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Tue Mar 06 2018 - 15:53:00 CST

Increase the margin or restart from where you've gotten to. I've used
margins up to 10 for systems that shrink alot in a particular dimension
in the first few ns, particularly if I padded the initial box size a
bit. Once the volume settles down and waters have been packed
accurately, you can set the margin to a lower value if you notice a real
performance impact, although I tend not to.

-Josh

On 03/06/2018 02:47 PM, Ashutosh Shandilya wrote:
> Thanks, I used margin 3 after removing langevin piston it worked for (*nvt.in
> <https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fnvt.in&data=02%7C01%7CJoshua.Vermaas%40nrel.gov%7Cbf34ff8b122941680be808d583abcfe0%7Ca0f29d7e28cd4f5484427885aee7c080%7C0%7C0%7C636559696319365108&sdata=86oX0fTCjsfkxlIvhSNOTeYZNRiJD44xOezmZON4G3s%3D&reserved=0>*) but when I am trying to run npt it is still gives the
> same error (*Periodic cell has become too small for original patch grid!*).
> Attached are my input files, kindly have a look if I am missing something.
>
>
> Many thanks,
>
> Ashutosh
>
>
> On Tue, Mar 6, 2018 at 2:50 AM, Norman Geist <norman.geist_at_uni-greifswald.de
>> wrote:
>> You can just add a line:
>>
>>
>>
>> margin 3
>>
>>
>>
>> to the namd input file. This will mostly prevent namd from aborting on
>> large box shrink on the cost of performance. Therefore, after the 1st
>> initial shrink, you can restart the npt without margin since the box won’t
>> shrink that much again. Actually the reason why it shrinks so much
>> initially, is that the solvation tool you used (but almost all do) gave the
>> system a too small density.
>>
>>
>>
>> Norman
>>
>>
>>
>> *Von:* Ashutosh Shandilya [mailto:scfbioiitd_at_gmail.com]
>> *Gesendet:* Montag, 5. März 2018 22:04
>> *An:* Norman Geist <norman.geist_at_uni-greifswald.de>
>> *Betreff:* Re: namd-l: periodic cell has become too small for original
>> patch grid
>>
>>
>>
>> Thanks for your help. I switched off the Langevin piston (nvt.namd) and
>> it ran fine but now when I am switching to npt stepwise it has again the
>> same error. I am restarting with old coordinate, vel, xsc but still, the
>> problem persists. Could you explain how to you margin or any other
>> modification in the input file? I want to run a targeted MD and production
>> input file is also attached.
>>
>> Attached are my input files. Kindly have a look and suggest.
>>
>> Many thanks,
>>
>> Ash
>>
>>
>>
>> On Mon, Mar 5, 2018 at 3:17 AM, Norman Geist <norman.geist_at_uni-greifswald

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