Hello Satyajit,
I am sorry your email has not been answered before.
Some more information is needed in order to understand your problem better. Did you get an error in your NPT equilibration simulation? In the tutorial, constant pH MD is not performed during equilibration. It is only performed during the production phase of the simulation, which is ran in NVT. Thus, if icnstph is not set in your mdin file (or if it is set to 0), then you should not expect a cprestrt file.
I hope this helps,
Vinícius Wilian D Cruzeiro
PhD Candidate
Department of Chemistry, Physical Chemistry Division
University of Florida, United States
Voice: +1(352)846-1633<tel:+1(352)846-1633>
On Sep 5, 2020, at 12:16 AM, SATYAJIT KHATUA <satyajitkhatua09.gmail.com> wrote:
[External Email]
Dear Users,
I had raised a ticket regarding this problem that I
faced dated back to march 7th, 2020. Unfortunately, I couldn't able to
solve the problem till now and also didn't get any suggestions from any
users. So, I am mailing again to grab the user's attention in this regard.
Please help.
Thanks in advance,
Satyajit
Message: 4
Date: Sat, 7 Mar 2020 12:44:32 +0530
From: SATYAJIT KHATUA <satyajitkhatua09.gmail.com>
Subject: [AMBER] Unavailability of the file related to -cprestrt flag
in equilibration (NPT) step of constant pH MD in Amber14 with
AmberTools15
To: amber.ambermd.org
Message-ID:
<CAOoM83scVpX5C-hpBf==TneX4Rm5f4tesWe=97e4+bZCmdjqfw.mail.gmail.com>
Content-Type: text/plain; charset="UTF-8"
Dear Users,
I am doing a const pH MD simulations of an enzyme in
explicit solvent and I have followed this tutorial
https://urldefense.proofpoint.com/v2/url?u=http-3A__jswails.wikidot.com_explicit-2Dsolvent-2Dconstant-2Dph-2Dmd&d=DwICAg&c=sJ6xIWYx-zLMB3EPkvcnVg&r=vg8iTdivJL1PEwCvcH8P2DFF-Rtc9lAQvIqnaSWm1Pc&m=nGOAUe2dULeQMc_syIjuWyamMitar9rjTqwfSnfp6B8&s=mHiKbnmnmo75XQF6qavvU0wlpV72kbnC5_Xh0cuDk-g&e= for system
preparation as well as for inputs. And for running simulation followed the
tutorial provided in Amber advanced tutorials section
https://urldefense.proofpoint.com/v2/url?u=https-3A__ambermd.org_tutorials_advanced_tutorial18_section2.htm&d=DwICAg&c=sJ6xIWYx-zLMB3EPkvcnVg&r=vg8iTdivJL1PEwCvcH8P2DFF-Rtc9lAQvIqnaSWm1Pc&m=nGOAUe2dULeQMc_syIjuWyamMitar9rjTqwfSnfp6B8&s=Dm2sSHxpLachnToDgApZwcKedTvp2VPPyp6OcFkW_PA&e= . Up to
heating it seems that there was no problem as it generated all required
files without showing any kind of errors. But when I ran equilibration using
NPT ensemble, there was no file which supposed to be created by -cprestrt
flag. I have tried pmemd modules (both Cuda and Cuda.MPI) of AMBER for the
run, however, the problem persists. Can someone tell me what I have done
wrong here? Please help.
Thanks a lot,
Satyajit
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Received on Sat Sep 05 2020 - 10:30:02 PDT
