Dear All
I performed a solvent minimization on a protein system prepared using *H++*
web server for determining protonation states, followed by *pdb4amber*,
*reduce*, and finally *tleap* for solvating and force-field assignment
(protein.ff19SB, water.opc, OPCBOX, 14.0 Angstrom).
The following is the result of the solvent minimization (with *pmemd.MPI*)
############## FINAL RESULTS #############
NSTEP ENERGY RMS GMAX NAME
NUMBER
164 -1.2726E+05 2.0382E+01 8.9842E+01 O
42950
BOND = 106.0616 ANGLE = 673.0642 DIHED
= 1377.6394
UB = 0.0000 IMP = 0.0000
CMAP = 240.1635
VDWAALS = 9671.2400 EEL = -156522.0452 HBOND =
0.0000
1-4 VDW = 1507.9306 1-4 EEL = 15040.7857 RESTRAINT =
642.0222
EAMBER = -127905.1601
***** REPEATED LINMIN FAILURE *****
################ INPUT #####################
&cntrl
imin = 1, maxcyc = 5000, // LINMIN failure messages even at
maxcyc = 5000
ncyc = 50, ntx = 1, // Segfault at ncyc = 20. No
Segfault at ncyc = 50
ntwe = 0, ntwr = 500, ntpr = 50,
ntc = 2, ntf = 2, ntb = 1, ntp = 0,
cut = 8.0, // Scale 1-10, 1 being
"overkill", 10 used in tutorial
ntr=1, restraintmask = ':1-302' // All 300 residues restrained
restraint_wt = 100.0, // To be subsequently
"tapered-off"
ioutfm=1, ntxo=2,
/
#############################################
Based on the above (hopefully sufficient) I have these queries:
(1) Is an RMS value of 2.0382E+01 normal?
(2) Can LINMIN failure be responsible for, or correlated to, high RMS? Is
continually increasing *maxcyc* a sound way to resolve it? If so how can it
be resolved?
(3) Could delaying the conjugate gradient (*ncyc* 20 --> 50) adversely
affect the subsequent relaxation as well as production simulation?
Thanks and regards
-Nitin
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Received on Tue Nov 15 2022 - 00:30:03 PST
