Re: [AMBER] Replica exchange in explicit solvent

From: Cruzeiro,Vinicius Wilian D <vwcruzeiro.ufl.edu>
Date: Fri, 13 Apr 2018 19:36:20 +0000

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
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