Dear Amber Community,
I was trying to do the free energy calculation of the system I’m studying using the Thermodynamic Integration Technique. I changed the code given in the Tutorial a little bit according to my system. But the calculation stops after running for some time. I have attached the output that I am getting. It would be great if you could help. If any more information is needed I will gladly provide it
File Assignments:
| MDIN: mdin_min_v0_l0.02
| MDOUT: Nd_IL3_min_v0_l0.02.out
|INPCRD: Nd_IL3_0.rst
| PARM: Nd_IL3.prmtop
|RESTRT: Nd_IL3_min_v0_l0.02.rst
| REFC: Nd_IL3_0.rst
| MDVEL: mdvel.000
| MDFRC: mdfrc.000
| MDEN: mden.000
| MDCRD: mdcrd.000
|MDINFO: mdinfo.000
| MTMD: mtmd
|INPDIP: inpdip
|RSTDIP: rstdip
|INPTRA: inptraj
| REMLOG: rem.log
| REMTYPE: rem.type
| REMSTRIP:
| SAVEENE: saveene
|CLUSTERINF: cluster.info
| RESERVOIR: reserv/frame
| REMDDIM:
Here is the input file:
minimization
&cntrl
imin=1,
ncyc=1000,
ntmin=2,
maxcyc=5000,
ntpr=50,
cut=10.0,
iwrap=1,
ntr=1,
icfe=1,
clambda = 0.02,
ifsc=1,
scmask=':Nd',
/
--------------------------------------------------------------------------------
1. RESOURCE USE:
--------------------------------------------------------------------------------
| Flags: MPI
getting new box info from bottom of inpcrd
| INFO: Old style inpcrd file read
| peek_ewald_inpcrd: Box info found
|Largest sphere to fit in unit cell has radius = 20.946
| New format PARM file being parsed.
| Version = 1.000 Date = 07/30/24 Time = 12:41:18
NATOM = 4813 NTYPES = 12 NBONH = 2700 MBONA = 1959
NTHETH = 5850 MTHETA = 2259 NPHIH = 8250 MPHIA = 2250
NHPARM = 0 NPARM = 0 NNB = 22222 NRES = 304
NBONA = 1959 NTHETA = 2259 NPHIA = 2250 NUMBND = 12
NUMANG = 19 NPTRA = 11 NATYP = 13 NPHB = 0
IFBOX = 1 NMXRS = 25 IFCAP = 0 NEXTRA = 0
NCOPY = 0
| Memory Use Allocated
| Real 1244270
| Hollerith 14745
| Integer 683637
| Max Pairs 462048
| nblistReal 57756
| nblist Int 243000
| Total 15654 kbytes
| 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.
| Duplicated 0 dihedrals
| Duplicated 0 dihedrals
BOX TYPE: RECTILINEAR
--------------------------------------------------------------------------------
2. CONTROL DATA FOR THE RUN
--------------------------------------------------------------------------------
default_name
General flags:
imin = 1, nmropt = 0
Nature and format of input:
ntx = 1, irest = 0, ntrx = 1
Nature and format of output:
ntxo = 2, ntpr = 50, ntrx = 1, ntwr = 1
iwrap = 1, ntwx = 0, ntwv = 0, ntwe = 0
ioutfm = 1, ntwprt = 0, idecomp = 0, rbornstat= 0
Potential function:
ntf = 1, ntb = 1, igb = 0, nsnb = 25
ipol = 0, gbsa = 0, iesp = 0
dielc = 1.00000, cut = 10.00000, intdiel = 1.00000
Frozen or restrained atoms:
ibelly = 0, ntr = 1
restraint_wt = 0.00000
Energy minimization:
maxcyc = 5000, ncyc = 1000, ntmin = 2
dx0 = 0.01000, drms = 0.00010
Free energy options:
icfe = 1, ifsc = 1, klambda = 1
clambda = 0.0200, scalpha = 0.5000, scbeta = 12.0000
sceeorder = 2 dvdl_norest = 0
dynlmb = 0.0000 logdvdl = 0
Ewald parameters:
verbose = 0, ew_type = 0, nbflag = 1, use_pme = 1
vdwmeth = 1, eedmeth = 1, netfrc = 0
Box X = 42.294 Box Y = 41.892 Box Z = 44.502
Alpha = 90.000 Beta = 90.000 Gamma = 90.000
NFFT1 = 48 NFFT2 = 45 NFFT3 = 45
Cutoff= 10.000 Tol =0.100E-04
Ewald Coefficient = 0.27511
Interpolation order = 4
| MPI Timing options:
| profile_mpi = 0
LOADING THE CONSTRAINED ATOMS AS GROUPS
5. REFERENCE ATOM COORDINATES
defa
Kind Regards,
Sandaruwani Weerawarna
Graduate Student
Dr. Theresa Windus Lab
Department of Chemistry
Iowa State University
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Received on Thu Aug 08 2024 - 09:00:01 PDT
