Dear Amber users,
I’m running a molecular dynamics simulation of a protein with its ligand (which has three phosphates), a Mg+2 ion and three water molecules.
After successfully minimising the structure quantum mechanically (RMS=2.25E-02 and GMAX=6.75E-01) and “heating” the explicit solvent as in tutorial B1, I run the molecular dynamics treating a few residues, the Mg ion and the three water molecules quantum mechanically, like during the minimisation.
As I‘m looking for a reaction to proceed in the QM region, I remove the shake options from it with a noshakemask and, as the three water molecules are involved in this reaction, I also add jfastw=4, as advised in the manual in order to effectively remove the shake options from water molecules.
Here is the input file:
Constant Temp 300K MD
&cntrl
imin=0,
irest=1, ntx=7,
ntb=2, pres0=1.0, ntp=1, taup=1.0,
cut=12.0,
tempi=300.0, temp0=300.0,
ntt=3, gamma_ln=2.0,
nstlim=50000, dt=0.0005,
ntpr=100, ntwx=10, ntwr=1000,
ntc=2, ntf=2, jfastw=4,
noshakemask = '.900-909,917-933,2645,2646-2689,2828-2851,2931-2939',
ntr=1,
restraintmask = ':170,185,@CA,C,N',
restraint_wt=5.0,
ifqnt=1,
/
&qmmm
qmmask=':59,61,168,169,186-188',
qmcharge=-2,
qm_theory='PM3',
qmshake=0,
qmcut=12.0,
/
I guess that because of the thousands of water molecules present in the system, I get the error message “vlimit exceeded” from the first step.. So I wonder, is there any way to remove the shake options from the three water molecules in the QM region only and keep them in the rest of the solvent?
Thanks in advance for any suggestion,
Ruth
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Received on Fri Sep 25 2015 - 07:00:03 PDT
