AMBER Archive (2003)

Subject: Re: MD went crazy

From: Carlos Simmerling (carlos_at_csb.sunysb.edu)
Date: Fri Apr 18 2003 - 10:20:07 CDT

please provide output that lists the energies
at the first step- by the time we see what is going
on, it already has the vlimit warnings. it is important
to see the first step restraint energies, and how quickly
the energies rise, etc.
===================================================================
Carlos L. Simmerling, Ph.D.
Assistant Professor Phone: (631) 632-1336
Center for Structural Biology Fax: (631) 632-1555
Stony Brook University Web: http://comp.chem.sunysb.edu/carlos
Stony Brook, NY 11794-5115 E-mail: carlos.simmerling_at_stonybrook.edu
===================================================================

----- Original Message -----
From: "Youyi Peng" <pengyo_at_UMDNJ.EDU>
To: <amber_at_heimdal.compchem.ucsf.edu>
Sent: Friday, April 18, 2003 11:20 AM
Subject: MD went crazy

> Hi,
> I initiated MD by heating the ligand-protein complex with no
> constraints on the atoms from 0 to 300K in 10 ps.Then 100ps eqilibration
> at the constant temp. 300K was performed on restrained backbone and
> distance. I got crazy MD output. THe energy and temp. went to very high
> and a lot of vlimit warnings. Below is the input file and part of the
> output file. Please take a look for me.
> Thank you very much and happy good Friday!
>
> MDIN:
> dynamics w/o belly on protein, 9.0 cut, with constraints of backbone and
> distance
> &cntrl
> nmropt = 1,
> ntx = 5, irest = 1, ntrx = 1, ntxo = 1,
> ntpr = 1000, ntwx = 1000, ntwv = 0, ntwe = 0,
>
> ntf = 1, ntb = 0,
> cut = 9.0, nsnb = 10, dielc=4.0
>
> ibelly = 0, ntr = 1,
>
> imin = 0,
> nstlim = 100000,
> nscm = 0, dt = 0.001,
>
> temp0 = 300.0, tempi = 300.0,
> heat = 0.0,
> ntt = 1,
> tautp = 2.0,
> vlimit = 20.0,
>
>
> ntc = 1, tol = 0.00001,
> &end
>
> &ewald
> eedmeth=5,
> &end
>
> &wt
> type='END' ,
> &end
>
> LISTOUT=POUT
> DISANG=RST.dist
>
> Hold the backbone restrainted
> 500.0
> FIND
> * CT * *
> * N * *
> * C * *
> * O * *
> SEARCH
> RES 1 293
> END
> END
>
> OUTPUT
> vlimit exceeded for step 992; vmax = 1297679.08
> vlimit exceeded for step 993; vmax = 200557512.
> vlimit exceeded for step 994; vmax = 86296.6221
> vlimit exceeded for step 995; vmax = 530655.444
> vlimit exceeded for step 996; vmax = 719129.926
> vlimit exceeded for step 997; vmax = 2.54845046E+09
> vlimit exceeded for step 998; vmax = 97404.1622
> vlimit exceeded for step 999; vmax = 330667.274
>
> NSTEP = 1000 TIME(PS) = 11.000 TEMP(K) =********* PRESS = 0.0
>
> Etot = ************ EKtot = ************ EPtot =
> 3906732.9101
> BOND = 865895.1848 ANGLE = 223527.1116 DIHED =
> 15612.3010
> 1-4 NB = 1509819.0853 1-4 EEL = 546.5250 VDWAALS =
> 163607.4823
> EELEC = -1106.9859 EHBOND = 0.0000 RESTRAINT =
> 1128832.2060
> EAMBER (non-restraint) = 2777900.7040
>
>
>
>
>
>
>