# Re: [AMBER] How to gradually release the Cartesian restraint?

From: Mohamed Aboelnga <mohamed.aboelnga.uwaterloo.ca>
Date: Tue, 2 Nov 2021 18:49:30 +0000

Hi,

I still see ntr= 1 in both your input files. If you wan to conduct unrestrained heating you should have ntr = 0 instead.

Also, if you want to gradually decrease the wt of restraint, you need to decrease restraint_wt from its current value. See for 5 kcal/mol this parameter should be restraint_wt = 5.0. Similarly for the following subsequent heating, keep decreasing this restraint_wt value until zero.

Hope this helps,
Mohamed

________________________________
Sent: Tuesday, November 2, 2021 12:59:09 PM
To: amber.ambermd.org <amber.ambermd.org>
Subject: [AMBER] How to gradually release the Cartesian restraint?

Hi Amber staff,

I tried to gradually heat my system with a Cartesian restraint on my protein and ligand successfully.

Heating
&cntrl
imin = 0,
ig = -1,
ntx = 1,
irest = 0,
ntpr = 5000,
ntwx = 5000,
ntwr = 20000,
ntf = 2,
ntc = 2,
ntb = 1,
cut = 9.0,
nstlim = 3750000,
nscm = 10000,
dt = 0.004,
tempi = 0.0,
temp0 = 300.0,
ntt = 3,
gamma_ln = 2.0,
ntr = 1,
nmropt = 1,
restraint_wt = 10.0,
/
&wt type='REST', istep1=0, istep2=3750000, value1=10.0, value2=10.0 / #put restraint on immediately when starts md
&wt type='TEMP0', istep1=0, istep2=3750000, value1=0.0, value2=300.0 / #warm up the water and ion first gradually
&wt type='END' /

A V E R A G E S O V E R 750 S T E P S

NSTEP = 3750000 TIME(PS) = 15000.000 TEMP(K) = 150.27 PRESS = 0.0
Etot = -102763.2479 EKtot = 9201.2007 EPtot = -111964.4486
BOND = 370.8763 ANGLE = 903.3415 DIHED = 2206.8748
1-4 NB = 648.0782 1-4 EEL = 6292.2085 VDWAALS = 16618.0568
EELEC = -139303.3251 EHBOND = 0.0000 RESTRAINT = 299.4403
EAMBER (non-restraint) = -112263.8890
------------------------------------------------------------------------------

NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000

However, I failed to gradually release my Cartesian restraint. It does not release the Cartesian restraint at all.

Heating Release
&cntrl
imin = 0,
ig = -1,
ntx = 5,
irest = 1,
ntpr = 5000,
ntwx = 5000,
ntwr = 20000,
ntf = 2,
ntc = 2,
ntb = 1,
cut = 9.0,
nstlim = 8750000,
nscm = 10000,
dt = 0.004,
tempi = 300.0,
temp0 = 300.0,
ntt = 3,
gamma_ln = 2.0,
ntr = 1,
nmropt = 1,
restraint_wt = 10.0,
/
&wt type='REST', istep1=0, istep2=5000000, value1=10.0, value2=0 / #gradually release the restraint on protein and ligand, so the warm water heats the protein and ligand gradually
&wt type='REST', istep1=5000001, istep2=8750000, value1=0, value2=0 /
&wt type='TEMP0', istep1=0, istep2=5000000, value1=300.0, value2=300.0 / #keep the same temperature for the system
&wt type='TEMP0', istep1=5000001, istep2=8750000, value1=300.0, value2=300.0 /
&wt type='END' /

A V E R A G E S O V E R 1750 S T E P S

NSTEP = 8750000 TIME(PS) = 50000.000 TEMP(K) = 300.11 PRESS = 0.0
Etot = -77226.8740 EKtot = 18375.6561 EPtot = -95602.5300
BOND = 650.4447 ANGLE = 1446.3790 DIHED = 2311.4445
1-4 NB = 682.1081 1-4 EEL = 6283.5469 VDWAALS = 11123.8881
EELEC = -118795.6753 EHBOND = 0.0000 RESTRAINT = 695.3339
EAMBER (non-restraint) = -96297.8639
------------------------------------------------------------------------------

NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000

How can I gradually release my cartesian restraint?

Bw,
Heng

University of Manchester, PhD student .
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Received on Tue Nov 02 2021 - 12:00:02 PDT
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