It looks like you turned on positional restraints (ntr=1) but may not have
defined which atoms and what force constant.
On Thu, Aug 8, 2024, 11:48 AM Weerawarna Kurukulasooriy, Sandaruwani
Tharaka [CHEM] via AMBER <amber.ambermd.org> wrote:
> 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 - 09:30:02 PDT
