Hi All,
I am running the implicit solvent simulation, everything works without any
error until the "production" step. The simulation stops at production
without giving any error message!!!
==================================================================
this my "run" file:
==================================================================
#min
pmemd.cuda -O -i min1.in -o "$MOL"_min.out -c "$MOL".crd -p "$MOL".top -r
"$MOL"_min.rst -ref "$MOL".crd
#heat1
pmemd.cuda -O -i heat.gb300k.mdin -o "$MOL"_heat1.out -c "$MOL"_min.rst -p
"$MOL".top -r "$MOL"_heat1.rst -ref "$MOL"_min.rst -x "$MOL"_heat1.mdcrd
-ref "$MOL"_min.rst
#equilibrate 1
pmemd.cuda -O -i equil1.gb300k.mdin -o "$MOL"_equil1.out -c
"$MOL"_heat1.rst -p "$MOL".top -r "$MOL"_equil1.rst -ref "$MOL"_heat1.rst
-x "$MOL"_equil1.mdcrd -ref "$MOL"_heat1.rst
#equilibrate 2
pmemd.cuda -O -i equil2.gb300k.mdin -o "$MOL"_equil2.out -c
"$MOL"_equil1.rst -p "$MOL".top -r "$MOL"_equil2.rst -ref "$MOL"_equil1.rst
-x "$MOL"_equil2.mdcrd -ref "$MOL"_equil1.rst
#md
pmemd -O -i "$MOL".in -o "$MOL"_HS.md1.out -c "$MOL"_equil2.rst -p
"$MOL".top -r "$MOL"_HS.md1.rst -ref "$MOL"_equil2.rst -x
"$MOL"_HS.md1.traj -e ${MOL}.prod1.mden
pmemd -O -i "$MOL".in -o "$MOL"_HS.md2.out -c "$MOL"_HS.md1.rst -p
"$MOL".top -r "$MOL"_HS.md2.rst -ref "$MOL"_HS.md1.rst -x
"$MOL"_HS.md2.traj -e ${MOL}.prod2.mden
pmemd -O -i "$MOL".in -o "$MOL"_HS.md3.out -c "$MOL"_HS.md2.rst -p
"$MOL".top -r "$MOL"_HS.md3.rst -ref "$MOL"_HS.md2.rst -x
"$MOL"_HS.md3.traj -e ${MOL}.prod3.mden
pmemd -O -i "$MOL".in -o "$MOL"_HS.md4.out -c "$MOL"_HS.md3.rst -p
"$MOL".top -r "$MOL"_HS.md4.rst -ref "$MOL"_HS.md3.rst -x
"$MOL"_HS.md4.traj -e ${MOL}.prod4.mden
pmemd -O -i "$MOL".in -o "$MOL"_HS.md5.out -c "$MOL"_HS.md4.rst -p
"$MOL".top -r "$MOL"_HS.md5.rst -ref "$MOL"_HS.md4.rst -x
"$MOL"_HS.md5.traj -e ${MOL}.prod5.mden
======================================================================
This my "production" input file:
======================================================================
Hexosome md
&cntrl
imin = 0, irest=1, ntx=5, ig=-1,
ntc=2, ntf=2,
igb = 5, gbsa = 0,
ntpr = 1000, ntwx = 1000, ntwr=1000,
ntt = 3, gamma_ln = 0.01,
temp0 = 380.0,
nstlim = 14000000, dt = 0.002,
cut = 9999.0, ntb = 0,
saltcon = 1.0,
ntr=1,
restraint_wt=10.0,
restraintmask=':1-294,333-429,449-531,552-642,684-782,818-916,940-1018,1037-1133,1172-1268'
/
END
========================================================================
This the end of "Production" out put file:
========================================================================
| MDFRC: mdfrc
Here is the input file:
Hexosome md
&cntrl
imin = 0, irest=1, ntx=5, ig=-1,
ntc=2, ntf=2,
igb = 5, gbsa = 0,
ntpr = 20000, ntwx = 20000, ntwr=-250000,
ntt = 3, gamma_ln = 0.01,
temp0 = 380.0,
nstlim = 14000000, dt = 0.0018,
cut = 9999.0, ntb = 0, saltcon = 1.0,
ntr=1,
restraint_wt=10.0,
restraintmask=':1-294,333-429,449-531,552-642,684-782,818-916,940-1018,1037-113
/
Note: ig = -1. Setting random seed to 355109 based on wallclock time in
microseconds.
| irandom = 1, using AMBER's internal random number generator (default).
| Conditional Compilation Defines Used:
| PUBFFT
| BINTRAJ
| EMIL
| New format PARM file being parsed.
| Version = 1.000 Date = 08/30/19 Time = 11:18:48
| Note: 1-4 EEL scale factors are being read from the topology file.
| Note: 1-4 VDW scale factors are being read from the topology file.
| INFO: Reading atomic numbers from topology file.
| Duplicated 0 dihedrals
| Duplicated 0 dihedrals
--------------------------------------------------------------------------------
1. RESOURCE USE:
--------------------------------------------------------------------------------
NATOM = 25093 NTYPES = 18 NBONH = 11486 MBONA = 14430
NTHETH = 26404 MTHETA = 20681 NPHIH = 52898 MPHIA = 52337
NHPARM = 0 NPARM = 0 NNB = 138904 NRES = 1268
NBONA = 14430 NTHETA = 20681 NPHIA = 52337 NUMBND = 103
NUMANG = 244 NPTRA = 230 NATYP = 43 NPHB = 0
IFBOX = 0 NMXRS = 33 IFCAP = 0 NEXTRA = 0
NCOPY = 0
Implicit solvent radii are H(N)-modified Bondi radii (mbondi2)
--------------------------------------------------------------------------------
========================================================================
This end of "equlilbrium" out put:
========================================================================
NSTEP = 100000 TIME(PS) = 600.000 TEMP(K) = 378.33 PRESS =
0.0
Etot = -49173.7535 EKtot = 23980.4375 EPtot =
-73154.1910
BOND = 6448.0438 ANGLE = 14545.2846 DIHED =
20643.0184
1-4 NB = 5822.1040 1-4 EEL = 1641.2393 VDWAALS =
-13633.5621
EELEC = -1352.7147 EGB = -113486.4374 RESTRAINT =
6218.8332
EAMBER (non-restraint) = -79373.0242
------------------------------------------------------------------------------
A V E R A G E S O V E R 100 S T E P S
NSTEP = 100000 TIME(PS) = 600.000 TEMP(K) = 380.10 PRESS =
0.0
Etot = -48843.5987 EKtot = 24092.2032 EPtot =
-72935.8019
BOND = 6551.5153 ANGLE = 14632.4253 DIHED =
20671.0942
1-4 NB = 5829.4865 1-4 EEL = 1560.6349 VDWAALS =
-13611.0618
EELEC = -1594.5137 EGB = -113173.6268 RESTRAINT =
6198.2442
EAMBER (non-restraint) = -79134.0461
------------------------------------------------------------------------------
R M S F L U C T U A T I O N S
NSTEP = 100000 TIME(PS) = 600.000 TEMP(K) = 2.03 PRESS =
0.0
Etot = 207.3262 EKtot = 128.8086 EPtot =
152.3245
BOND = 68.7550 ANGLE = 106.8440 DIHED =
49.1484
1-4 NB = 31.5357 1-4 EEL = 90.7258 VDWAALS =
34.0266
EELEC = 490.4707 EGB = 478.4659 RESTRAINT =
51.2432
EAMBER (non-restraint) = 101.0813
------------------------------------------------------------------------------
--------------------------------------------------------------------------------
5. TIMINGS
--------------------------------------------------------------------------------
| NonSetup CPU Time in Major Routines:
|
| Routine Sec %
| ------------------------------
| Nonbond 650.31 99.67
| Bond 0.00 0.00
| Angle 0.00 0.00
| Dihedral 0.00 0.00
| Shake 1.03 0.16
| RunMD 1.11 0.17
| Other 0.00 0.00
| ------------------------------
| Total 652.45
| Generalized Born CPU Time:
|
| Routine Sec %
| ------------------------------------
| Radii Calc 0.00 0.00
| Diagonal Calc 0.00 0.00
| Off Diagonal Calc 0.00 0.00
| GBSA LCPO Calc 0.00 0.00
| ---------------------------------
| Total 0.00 0.00
| Final Performance Info:
| -----------------------------------------------------
| Average timings for last 1 steps:
| Elapsed(s) = 0.00 Per Step(ms) = 0.90
| ns/day = 190.98 seconds/ns = 452.39
|
| Average timings for all steps:
| Elapsed(s) = 689.04 Per Step(ms) = 6.89
| ns/day = 25.08 seconds/ns = 3445.18
| -----------------------------------------------------
| Setup CPU time: 2.05 seconds
| NonSetup CPU time: 652.45 seconds
| Total CPU time: 654.50 seconds 0.18 hours
| Setup wall time: 2 seconds
| NonSetup wall time: 689 seconds
| Total wall time: 691 seconds 0.19 hours
========================================================================
I tried use the "fiel.crd" my coordinate fiel as "reference" fiel, but got
the same probel.
What is the problem?
--
Parviz Seifpanahi
Ph.D. Candidate
Department of Physics
Virginia Tech, Blacksburg, Va 24061
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Received on Mon Sep 09 2019 - 15:30:02 PDT
