Re: [AMBER] restarting REMD vacuum simulation with watercap

From: Cruzeiro,Vinicius Wilian D <>
Date: Tue, 19 Jun 2018 20:43:54 +0000

Hello Tran,

Thanks for pointing this issue out. I will prepare a patch with a fix for this asap. Also, I will send you off-list some instructions so you may restart your simulation right away.

All the best,

Vinícius Wilian D Cruzeiro

PhD Candidate
Department of Chemistry, Physical Chemistry Division
University of Florida, United States

Voice: +1(352)846-1633

From: Duy Tran Phuoc <>
Sent: Monday, June 18, 2018 11:25:56 PM
Subject: [AMBER] restarting REMD vacuum simulation with watercap

Dear AMBER users and developers,
Recently I got problem in restarting REMD vaccum simulation after 500ns
running of 16 replica in AMBER 17 using sander.MPI.
The simulation setting is below:
   imin = 0, irest = 1, ntx = 5,
   ntb = 0,igb=0,nscm=100000000,
   cut = 999.0, rgbmax=999.0, ntr = 1,
   ntc = 2, ntf = 2, iwrap =0, ioutfm = 1,
   temp0=180.00 ,ig=-1,
   ntt = 3, gamma_ln = 1.0,
   nstlim=500, dt=0.002,
   ntpr=100, ntwx=500, ntwr=5000, ntxo =2,
   ivcap=0, fcap=100.0,
 &wt TYPE='END'

After finishing 500ns simulation, I try to run more 500ns but receiving the
following message from AMBER 17

| ERROR: The box sizes do not match for all REMD replicas.
           This can happen, for example, if you are using different input
coordinate files
           for the different replicas and these structures come from a NPT
           Make sure the box lengths and angles are the same for all
replicas in all input
           coordinate files.


Because I do not use periodic box in this simulation, this message is very
To confirm this is not the error from my setup, I try to restart without
REMD (normal MD), and they ran smoothly.

Can anyone help me to overcome this.
Thank you in advance.

Tran Phuoc Duy
Tokyo Institute of Technology
School of Life Science and Technology
Kitao laboratory
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Received on Tue Jun 19 2018 - 14:00:03 PDT
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