Hello Maya,
The cpin file will not be read unless icnstph=1 or 2, thus it was not read during your equilibration. The cpin file for a implicit solvent simulation is not going to be the same as for a explicit solvent simulation. Did you use cpinutils.py to generate a new cpin for the explicit solvent simulation? Just for testing, try to run a single simulation with icnstph=2 and without pH-REMD just to see it works.
Best,
Vinícius Wilian D Cruzeiro
PhD Candidate
Department of Chemistry, Physical Chemistry Division
University of Florida, United States
Voice: +1(352)846-1633
________________________________
From: Maya Hauss <lordofthebhokaral.gmail.com>
Sent: Friday, April 13, 2018 3:23:12 PM
To: amber.ambermd.org
Subject: [AMBER] Replica exchange in explicit solvent
Hi,
I have been trying to combine the tutorials for ph replica exchange in
implicit solvent (
https://urldefense.proofpoint.com/v2/url?u=http-3A__jswails.wikidot.com_ph-2Dremd&d=DwICAg&c=pZJPUDQ3SB9JplYbifm4nt2lEVG5pWx2KikqINpWlZM&r=LIQu8OlVNKmzfbMg9_5FnKrt9-DrdQBJXyFyocKAWXc&m=esjmUA8TbB6C6-FJ5Gm2efvFMjQdHImdZCKZOaUz1Pw&s=t3Gkpr5qQeV7_VDSF0PD923Fo2KRjqs2rolAbwO5uAQ&e=), and constant ph
simulations in explicit solvent (
https://urldefense.proofpoint.com/v2/url?u=http-3A__jswails.wikidot.com_&d=DwICAg&c=pZJPUDQ3SB9JplYbifm4nt2lEVG5pWx2KikqINpWlZM&r=LIQu8OlVNKmzfbMg9_5FnKrt9-DrdQBJXyFyocKAWXc&m=esjmUA8TbB6C6-FJ5Gm2efvFMjQdHImdZCKZOaUz1Pw&s=UccR2VU_W3NDpX4pPiPHHJJZFOC2euDVE665NDel07s&e=
explicit-solvent-constant-ph-md) to perform replica exchange in explicit
solvent.
I used the following input file for my production run
imin=0, irest=1, ntx=5, ntxo = 2
ntpr=1000, ntwx=1000, nstlim=3000,
dt=0.002, ntt=3, tempi=300,
icnstph=2, ntcnstph=100, ntrelax=200,
solvph=8.0, saltcon=0.1, temp0=300.0,
ntc=2, ntf = 2, gamma_ln=1.0, ig=-1, ntp=1,
cut=8, ntb=2, iwrap=1, ioutfm=1,
However, whenever i include the icnstph=2 parameter, I get the following
error
message *"forrtl: severe (18): too many values for NAMELIST variable" *
pointing
to the input cpin file. I did not have any problems using the same cpin file
for the equilibriation run without the icnstph=2 parameter, or with the
entire imlicit solvent tutorial.I am not sure if I am doing something wrong
in combining the two tutorials. Would appreciate help with this issue. I am
using amber 16 update13.
Maya
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Received on Fri Apr 13 2018 - 13:00:02 PDT
