Dear All,
I ran MD with 10, 15 and 30A TIP3PBOX to understand the effect of box size
on relative FF energies between two systems.
The calculations when well with 10 and 15A box size.
But I'm getting the following error in mdout file with the system setup
with 30A TIP3PBOX.
I tried by reducing the cut values 9999, 999, 199 and 99 but got the same
error message. For the 30A system the box size is > 100 A and 32414 waters
(tleap output pasted below).
Can you please help me understand if this error is due to memory or some
other factor?
I can't find this variable in the manual and there is little info on the
archives about the same (
http://archive.ambermd.org/201101/0159.html).
Please do let me know if additional information is needed about my system
setup.
Looking forward to valuable suggestions from the list.
thank you and best regards
single point energy calculations of ferric state coordinates using ferrous
parameters
&cntrl
ntx=1, ntpr=1, ntwx=1,
imin=5, maxcyc=1, !Single-point energy calculation on each frame
ntb=0, !Non-periodic
cut=99., !Calculate all solute-solute interactions
/
--------------------------------------------------------------------------------
1. RESOURCE USE:
--------------------------------------------------------------------------------
| Flags: MPI
| NONPERIODIC ntb=0 and igb=0: Setting up nonperiodic simulation
|Largest sphere to fit in unit cell has radius = 78.915
| New format PARM file being parsed.
| Version = 1.000 Date = 02/19/21 Time = 21:23:34
NATOM = 99456 NTYPES = 19 NBONH = 98343 MBONA = 1148
NTHETH = 2507 MTHETA = 1581 NPHIH = 4977 MPHIA = 4857
NHPARM = 0 NPARM = 0 NNB = 141965 NRES = 32557
NBONA = 1148 NTHETA = 1581 NPHIA = 4857 NUMBND = 107
NUMANG = 252 NPTRA = 194 NATYP = 54 NPHB = 1
IFBOX = 1 NMXRS = 72 IFCAP = 0 NEXTRA = 0
NCOPY = 0
| CMAP information read from topology file:
*Unreasonably large value for MAXPR: 0.49E+10*
truncated tleap output
--------------------------
Solute vdw bounding box: 37.769 41.632 46.477
Total bounding box for atom centers: 97.769 101.632 106.477
Solvent unit box: 18.774 18.774 18.774
Total vdw box size: *100.860 104.558 109.778* angstroms.
Volume: 1157694.469 A^3
Total mass 599714.586 amu, Density 0.860 g/cc
Added *32414* residues.
--
Regards,
Dr. Vaibhav A. Dixit,
Visiting Scientist at the Manchester Institute of Biotechnology (MIB), The
University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
AND
Assistant Professor,
Department of Pharmacy,
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Birla Institute of Technology and Sciences Pilani (BITS-Pilani),
VidyaVihar Campus, street number 41, Pilani, Rajasthan 333031.
India.
Phone No. +91 1596 255652, Mob. No. +91-7709129400,
Email: vaibhav.dixit.pilani.bits-pilani.ac.in, vaibhavadixit.gmail.com
http://www.bits-pilani.ac.in/pilani/vaibhavdixit/profile
https://www.linkedin.com/in/vaibhav-dixit-b1a07a39/
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Received on Fri Feb 19 2021 - 20:30:02 PST
