Hello Saikat,
I ran some tests here to double check and I believe there is no time mismatch between what the cpout and the mdout print. However, you need to have some cares in your calculation. The cpout will have a full record for the first and the last steps, and also for each step in which nstep%ntwx is zero. However, depending on your values of ntwx and ntcnstph, you will not have a full record in the cpout file for all frames of your trajectory.
For example, imagine that ntwx = 5 and ntcnstph = 2. The traj will be written for steps 0, 5, 10, 15, ..., but you will be doing protonation state change attempts for steps 0, 2, 4, 6, 8, 10, 12, ... Therefore, as the constant pH code will not be called at the steps 5, 15, 25, ... , you will only have full records in your cpout for steps 0, 10, 20, ... You can still find out the protonation states for steps 5, 15, 25, ... in your cpout file. For example, the protonation state at step 5 will still be the same as in step 4, however this information will not be in a full record, which would make your task to extract the information you want harder.
Therefore, to make things easier for you, you should make sure to choose ntwx and ntcnstph values in such a way that every time you write to the traj file you also make a protonation state change attempt to ensure that a full record will be written in the cpout file for all frames in your trajectory.
I hope this helps,
Best,
Vinícius Wilian D Cruzeiro
PhD Candidate
Department of Chemistry, Physical Chemistry Division
University of Florida, United States
Voice: +1(352)846-1633
________________________________
From: Saikat Dutta chowdhury <pbr322.dutta.gmail.com>
Sent: Thursday, April 5, 2018 8:33:07 AM
To: AMBER Mailing List
Subject: [AMBER] Query about Constant pH cpout file
Respected Sir/Ma'am,
I have performed a Constant pH simulation at pH 4.8 following the AMBER
tutorial and there is only one titratable residue in my peptide.
I have used ntwx=2500.
My goal is to extract the protonation state of the titratable residue for
all saved conformations during my production runs (saved at every 2500
steps).
For this, I tried to extract the information from "cpout" files because in
the manual it is written that "Full records are written on the first step
and every ntwx steps afterwards so as to coincide with the frames written
to the trajectory".
But when I looked into the cpout file I found there is a discrepancy in the
Time stamp. Bellow I have highlighted an example.
Solvent pH: 4.80000
Monte Carlo step size: 50
Time step: 25000000
Time: *50999.998*
Residue 0 State: 0
So my questions are:
1. Is this the way Amber writes protonation state information for the frame
saved at 51000ps?
2. Could I use the protonation state information saved for Time: 50999.998
in the cpout file for the frame saved for 51000ps?
Thank you,
Saikat
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Received on Thu Apr 05 2018 - 10:30:02 PDT
