From: Diship Srivastava (dishipsrivastava_at_gmail.com)
Date: Wed Dec 15 2021 - 23:42:58 CST
Hi,
Based on my previously asked question on the namd forum (
https://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2020-2021/1532.html),
I have written a tcl force script to apply harmonic constraints during
constant pH MD run. While the script works fine with normal MD run, when
constant pH option is turned on, NAMD crashes with "can't read "group1": no
such variable" error. How can I modify my script so that it works during
cphmd run.
Thanks in advance.
Tcl script can be found in attachment and a snippet of log file is as
follows:
TCL: namdcph) B:22:LYS : 7500 1.00
TCL: namdcph) B:27:GLU : 7500 1.00
TCL: namdcph) B:29:LYS : 7500 1.00
TCL: namdcph) *************************************************
psfgen) Info: writing psf file 5.5/namdcph.md.psf
psfgen) total of 50849 atoms
psfgen) total of 39142 bonds
psfgen) total of 42635 angles
psfgen) total of 43628 dihedrals
psfgen) total of 376 impropers
psfgen) total of 0 explicit exclusions
psfgen) total of 54 cross-terms
psfgen) Info: psf file complete.
psfgen) Info: writing pdb file 5.5/namdcph.md.pdb
psfgen) Info: pdb file complete.
psfgen) Info: writing namdbin file 5.5/namdcph.md.coor
psfgen) Info: writing velnamdbin file 5.5/namdcph.md.vel
psfgen) Info: namdbin file complete.
psfgen) Info: velnamdbin file complete.
TCL: namdcph) clearing extraBondsFile 5.5/namdcph.sw.extrabonds
TCL: Reloading molecular structure from file 5.5/namdcph.md.psf and pdb
file 5.5/namdcph.md.pdb
Info: TIME FOR READING PSF FILE: 5.84653
Info: READING EXTRA BONDS FILE 5.5/namdcph.sw.extrabonds
Info: Reading pdb file 5.5/namdcph.md.pdb
Info: TIME FOR READING PDB FILE: 0.0943979
Info:
Info: ****************************
Info: STRUCTURE SUMMARY:
Info: 50849 ATOMS
Info: 39142 BONDS
Info: 42635 ANGLES
Info: 43628 DIHEDRALS
Info: 376 IMPROPERS
Info: 54 CROSSTERMS
Info: 0 EXCLUSIONS
Info: 44345 RIGID BONDS
Info: 108202 DEGREES OF FREEDOM
Info: 17989 HYDROGEN GROUPS
Info: 4 ATOMS IN LARGEST HYDROGEN GROUP
Info: 17989 MIGRATION GROUPS
Info: 4 ATOMS IN LARGEST MIGRATION GROUP
Info: TOTAL MASS = 303558 amu
Info: TOTAL CHARGE = 7.00001 e
Info: MASS DENSITY = 1.00502 g/cm^3
Info: ATOM DENSITY = 0.101381 atoms/A^3
Info: *****************************
Info: ADDED 125405 IMPLICIT EXCLUSIONS
Info: NONBONDED TABLE R-SQUARED SPACING: 0.0625
Info: NONBONDED TABLE SIZE: 769 POINTS
Info: INCONSISTENCY IN FAST TABLE ENERGY VS FORCE: 0.000325096 AT 11.9556
Info: INCONSISTENCY IN SCOR TABLE ENERGY VS FORCE: 0.000324844 AT 11.9556
Info: ABSOLUTE IMPRECISION IN VDWA TABLE ENERGY: 9.6778e-33 AT 11.9974
Info: RELATIVE IMPRECISION IN VDWA TABLE ENERGY: 3.71539e-17 AT 11.9974
Info: INCONSISTENCY IN VDWA TABLE ENERGY VS FORCE: 0.0040507 AT 0.251946
Info: ABSOLUTE IMPRECISION IN VDWB TABLE ENERGY: 9.34011e-27 AT 11.9974
Info: RELATIVE IMPRECISION IN VDWB TABLE ENERGY: 2.98256e-17 AT 11.9974
Info: INCONSISTENCY IN VDWB TABLE ENERGY VS FORCE: 0.00150189 AT 0.251946
TCL: Reinitializing atom data from files with basename 5.5/namdcph.md
Info: Reading from binary file 5.5/namdcph.md.coor
Info: Reading from binary file 5.5/namdcph.md.vel
Info: REMOVING COM VELOCITY -0.0070921 0.0605137 -0.0096071
TCL: Minimizing for 100 steps
TCL: Line Number 30
TCL: can't read "group1": no such variable
-- Diship Srivastava SRF Department of Chemistry IIT(ISM) - Dhanbad India
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