Re: [AMBER] Interesting findings regarding water density, ntf values, and total potential energy

From: Liao <>
Date: Wed, 24 Nov 2021 01:04:57 +0800

Thanks for the suggestion Dave,
To create the input coordinates, I made a PDB file with only a single water molecule, and solvated the system in tleap. Box size was octahedral 30 A extended from solute (the water molecule)
Here is the mdin file, and the program is pmemd.cuda. In the 3 scenarios, ntf=1,2 or 8 is being changed. When ntf=2 or 8, shake must be turned on. If ntf=1 also has SHAKE turned on, the results are identical to ntf=2.
 MD simualation
 imin=0, ! Perform MD
 nstlim=50000 ! Number of MD steps
 ntb=2, ! 2=Constant Pressure, default when ntp>0. Unit cell size changes to keep P constant) (0=no periodicity applied and PME is off, default when igb>0)(1=constant volume, default when igb and ntp both 0)
 ntc=2, ! 2=SHAKE on for bonds with hydrogen (SHAKE restricts bond stretches) (3=on for all bonds, 1=off, see p352 manual)
 dt=0.001, ! Timestep (ps)
 ntp=1, ! 1=Isotropic pressure scaling (0=no scaling) (should be 1 or 2 when constant pressure periodic boundaries are used)
 barostat=1 ! 1=Berendsen barostat, 2=montecarlo thermostat, p339 amber manual, 2 is suppose to be faster when ntb=2
 taup=0.5 ! Pressure relaxtion time (ps)
 ntf=8, ! 2=No force evaluation for bonds with hydrogen (1=complete force evaluation)
 ntt=3, ! Langevin thermostat (0=constant total energy, p337 manual)
 gamma_ln=2 ! Collision Frequency for thermostat
 ig=-1, ! Random seed for thermostat
 temp0=300 ! Simulation temperature (K)
 ntwx= 10000, ! Write to trajectory file every ntwx steps
 ntpr= 1000, ! Print to mdout every ntpr steps
 ntwr= 10000, ! Write a restart file every ntwr steps
 cut=8, ! Nonbonded cutoff in Angstroms
 ntxo=2, ! 1=Write coordinate file in ASCII format, 2=NetCDF
 ioutfm=1, ! 0=Write trajectory file in ASCII format, 1=NetCDF
 nmropt=0, !

Sender:David A Case <>
Sent At:2021 Nov. 23 (Tue.) 08:03
Recipient:Liao <>; AMBER Mailing List <>
Subject:Re: [AMBER] Interesting findings regarding water density, ntf values, and total potential energy

On Tue, Nov 23, 2021, Liao wrote:

>I found out that the water density is affected by ntf values.

This is indeed odd. Can you post your mdin file (and what program you are
running: for pmemd, is it CPU or GPU)? How big is your water box?
How did you create it?

If we don't spot any problems with the mdin file, someone will have to try
to reproduce the result.


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Received on Tue Nov 23 2021 - 09:30:02 PST
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