Thanks Carlos, indeed I did not use iwrap=1. All is right.
Best,
Baptiste
Le 14/02/2020 à 12:34, Carlos Simmerling a écrit :
> There should be no need for you to add such a line to your rst7, it will be
> generated automatically if you set the ntb variable. Perhaps your solvent
> looks dispersed because you did not use iwrap=1? Try using cpptraj and
> autoimage on your trajectory.
> If this is not the problem then please send your entire input files
> starting from the first run.
>
> On Fri, Feb 14, 2020, 6:04 AM Baptiste Legrand <bap.legrand.gmail.com>
> wrote:
>
>> Dear all,
>>
>> I compared production run in NPT and NVT ensemble for a protein
>> complexe. I saved about 30% of time at constant volume. Nevertheless, as
>> I did not specified the volume of the solvent box as indicated in the
>> following tutorial:
>> https://ambermd.org/tutorials/advanced/tutorial21/section2.htm, and the
>> water molecules are dispersed in a large volume.
>>
>> Thus, I add the following line during the equilibration as indicated,
>> the box is not exactly cubic but rectangular:
>>
>> &ewald nfft1=80, nfft2=60, nfft3=60, order=4 /
>>
>> then I calculated the average box edge from the average volume =>
>> 61.3534403, then I converted the final ncrst to rst7 to modify the
>> latest restart file adding the box lengths as indicated.
>> As the box is not really cubic, is it a strong approximation to add
>> 61.3534403 61.3534403 61.3534403 90.0 90.0 90.0 in the rst7 file to
>> start the production run at NVT and where should I add this line?
>>
>> Thanks,
>>
>> Best regards
>>
>> Baptiste
>> IBMM, University of Montpellier
>>
>> ps: thanks again Elvis for your answer last week, I forgot to
>> re-activate the mail delivery for the amber list.
>>
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Received on Wed Feb 19 2020 - 00:30:02 PST
