Dear David,
Following to your comment I have corrected my min1.in script:
5f5b_gur: initial minimisation: solvent
&cntrl
imin = 1, iwrap = 1,
maxcyc = 40000,
ncyc = 5000,
ntb=1,
ntp=0,
ntf=1,
ntc=1,
ntpr=50,
ntwr=2000,
cut=10.0,
ntr=1, restraintmask=':1-1097',
restraint_wt=500.0
Unfortunately, I faced yet another problem -
the job reported Error termination. (see below the min1.out file).
I would appreciate your advice how to resolve the problem.
Thank you,
Michael
-------------------------------------------------------
Amber 14 SANDER 2014
-------------------------------------------------------
| PMEMD implementation of SANDER, Release 14
| Run on 08/30/2016 at 21:23:41
| Executable path: pmemd.cuda
| Working directory: /home/shokhen/Documents/amber_5f5b_11pep_3w_frm_gur_cl0_old/1_
| Hostname: Unknown
[-O]verwriting output
File Assignments:
| MDIN: min1.in
| MDOUT: min1.out
| INPCRD: ../mc.inpcrd
| PARM: ../mc.prmtop
| RESTRT: min1.rst
| REFC: refc
| MDVEL: mdvel
| MDEN: mden
| MDCRD: mdcrd
| MDINFO: mdinfo
| MDFRC: mdfrc
Here is the input file:
5f5b_gur: initial minimisation: solvent
&cntrl
imin = 1, iwrap = 1,
maxcyc = 40000,
ncyc = 5000,
ntb=1,
ntp=0,
ntf=1,
ntc=1,
ntpr=50,
ntwr=2000,
cut=10.0,
ntr=1, restraintmask=':1-1097',
restraint_wt=500.0
/
|--------------------- INFORMATION ----------------------
| GPU (CUDA) Version of PMEMD in use: NVIDIA GPU IN USE.
| Version 14.0.1
|
| 06/20/2014
|
| Implementation by:
| Ross C. Walker (SDSC)
| Scott Le Grand (nVIDIA)
|
| CAUTION: The CUDA code is currently experimental.
| You use it at your own risk. Be sure to
| check ALL results carefully.
|
| Precision model in use:
| [SPFP] - Mixed Single/Double/Fixed Point Precision.
| (Default)
|
|--------------------------------------------------------
|----------------- CITATION INFORMATION -----------------
|
| When publishing work that utilized the CUDA version
| of AMBER, please cite the following in addition to
| the regular AMBER citations:
|
| - Romelia Salomon-Ferrer; Andreas W. Goetz; Duncan
| Poole; Scott Le Grand; Ross C. Walker "Routine
| microsecond molecular dynamics simulations with
| AMBER - Part II: Particle Mesh Ewald", J. Chem.
| Theory Comput., 2013, 9 (9), pp3878-3888,
| DOI: 10.1021/ct400314y.
|
| - Andreas W. Goetz; Mark J. Williamson; Dong Xu;
| Duncan Poole; Scott Le Grand; Ross C. Walker
| "Routine microsecond molecular dynamics simulations
| with AMBER - Part I: Generalized Born", J. Chem.
| Theory Comput., 2012, 8 (5), pp1542-1555.
|
| - Scott Le Grand; Andreas W. Goetz; Ross C. Walker
| "SPFP: Speed without compromise - a mixed precision
| model for GPU accelerated molecular dynamics
| simulations.", Comp. Phys. Comm., 2013, 184
| pp374-380, DOI: 10.1016/j.cpc.2012.09.022
|
|--------------------------------------------------------
|------------------- GPU DEVICE INFO --------------------
|
| CUDA_VISIBLE_DEVICES: not set
| CUDA Capable Devices Detected: 2
| CUDA Device ID in use: 0
| CUDA Device Name: GeForce GTX TITAN
| CUDA Device Global Mem Size: 6143 MB
| CUDA Device Num Multiprocessors: 14
| CUDA Device Core Freq: 0.88 GHz
|
|--------------------------------------------------------
| Conditional Compilation Defines Used:
| PUBFFT
| BINTRAJ
| CUDA
| EMIL
| Largest sphere to fit in unit cell has radius = 45.214
| New format PARM file being parsed.
| Version = 1.000 Date = 08/04/16 Time = 14:23:26
| 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
--------------------------------------------------------------------------------
1. RESOURCE USE:
--------------------------------------------------------------------------------
getting new box info from bottom of inpcrd
NATOM = 84048 NTYPES = 24 NBONH = 67705 MBONA = 16004
NTHETH = 59050 MTHETA = 18078 NPHIH = 94915 MPHIA = 61695
NHPARM = 0 NPARM = 0 NNB = 283271 NRES = 15630
NBONA = 16004 NTHETA = 18078 NPHIA = 61695 NUMBND = 86
NUMANG = 188 NPTRA = 253 NATYP = 53 NPHB = 1
IFBOX = 1 NMXRS = 50 IFCAP = 0 NEXTRA = 0
NCOPY = 0
| Coordinate Index Table dimensions: 20 20 16
| Direct force subcell size = 5.6842 5.5229 5.6517
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 = 1, ntpr = 50, ntrx = 1, ntwr = 2000
iwrap = 1, ntwx = 0, ntwv = 0, ntwe = 0
ioutfm = 0, 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 = 500.00000
Energy minimization:
maxcyc = 40000, ncyc = 5000, ntmin = 1
dx0 = 0.01000, drms = 0.00010
| Intermolecular bonds treatment:
| no_intermolecular_bonds = 1
| Energy averages sample interval:
| ene_avg_sampling = 1
Ewald parameters:
verbose = 0, ew_type = 0, nbflag = 1, use_pme = 1
vdwmeth = 1, eedmeth = 1, netfrc = 0
Box X = 113.684 Box Y = 110.458 Box Z = 90.427
Alpha = 90.000 Beta = 90.000 Gamma = 90.000
NFFT1 = 120 NFFT2 = 112 NFFT3 = 96
Cutoff= 10.000 Tol =0.100E-04
Ewald Coefficient = 0.27511
Interpolation order = 4
LOADING THE CONSTRAINED ATOMS AS GROUPS
5. REFERENCE ATOM COORDINATES
Unit 10 Error on OPEN: refc
________________________________
From: David A Case <david.case.rutgers.edu>
Sent: Tuesday, August 30, 2016 6:26:12 PM
To: AMBER Mailing List
Subject: Re: [AMBER] frozen geometry setting?
On Tue, Aug 30, 2016, Michael Shokhen wrote:
> I have applied minimization with restraints (see script below).
> Unfortunately, protein residues change their geometry significantly.
Your restraints were never applied (see below), which should have been
clear from the mdout file.
>
> initial minimisation: solvent
> &cntrl
> imin = 1, iwrap = 1,
> maxcyc = 40000,
> ncyc = 5000,
> ntb=1,
> ntp=0,
> ntf=1,
> ntc=1,
> ntpr=50,
> ntwr=2000,
> cut=10.0,
> /
The above line ends the namelist; all further cards are ignored.
> ntr=1, restraintmask=':1-1097',
> restraint_wt=5000.0
Put the above two lines *into* the &cntrl namelist (before the "/" line.)
Consider using a restraint_wt two orders of magnitude smaller than what you
have here.
...good luck...dac
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Received on Tue Aug 30 2016 - 12:00:02 PDT
