AMBER Archive (2005)

Subject: Re: AMBER: Extended bonds-MD

From: Carlos Simmerling (carlos_at_ilion.bio.sunysb.edu)
Date: Wed Jun 15 2005 - 06:22:29 CDT

It sounds like it might be a problem with the file format in
the visualization. What program are you using? Are you telling
it that you have a periodic system? (crdbox in vmd; amber PBC in
moil-view, etc)

Ananda Rama Krishnan Selvaraj wrote:

>Dear Ross,
> As per you suggestion, i have changed the input parameter for
>the MD simulation in periodic boundary condition. but again i am getting
>that extended lines (extended bonds and totally deformed structures).
>here is the input
>
> PIB
>
>
>General flags:
> imin = 0, nmropt = 0
>
>Nature and format of input:
> ntx = 1, irest = 0, ntrx = 1
>
>Nature and format of output:
> ntxo = 1, ntpr = 200, ntrx = 1, ntwr =
> 500
> iwrap = 0, ntwx = 200, ntwv = 0, ntwe =
> 0
> ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat=
> 0
>
>Potential function:
> ntf = 2, ntb = 1, igb = 0, nsnb =
> 25
> ipol = 0, gbsa = 0
> dielc = 1.00000, cut = 8.00000, intdiel = 1.00000
> scnb = 2.00000, scee = 1.20000
>
>Frozen or restrained atoms:
> ibelly = 0, ntr = 1
>
>Molecular dynamics:
> nstlim = 100000, nscm = 1000, nrespa = 1
> t = 0.00000, dt = 0.00050, vlimit = 20.00000
>
>Temperature regulation:
> ig = 71277, ntt = 1, vrand = 0
> temp0 = 10.00000, tempi = 0.00000, heat = 0.00000
> dtemp = 5.00000, tautp = 1.00000
>
>SHAKE:
> ntc = 2, jfastw = 0
> tol = 0.00001
>
>Ewald parameters:
> verbose = 0, ew_type = 0, nbflag = 0, use_pme =
> 1
> vdwmeth = 1, eedmeth = 1, frc_int = 0, netfrc =
> 1
> Box X = 180.000 Box Y = 40.000 Box Z = 20.000
> Alpha = 90.000 Beta = 90.000 Gamma = 90.000
> NFFT1 = 180 NFFT2 = 40 NFFT3 = 20
> Cutoff= 8.000 Tol =0.100E-04
> Ewald Coefficient = 0.34864
> Interpolation order = 4
>
>The MD simulation was completed without any error message.
>Interestingly, every 102 steps (snop shots), i have observed good
>struture (comparatively, only one C-H bond is extended , other bonds are
>o.k).
>
>so could you tell the right way to correct error.
>
>
>moreover, i have started the simulation from the energy minimized
>structure ( it is o.k.)
>
>thanks....anand
>
>
>
>
>
>----- Original Message -----
>From: Ross Walker <ross_at_rosswalker.co.uk>
>Date: Tuesday, June 14, 2005 7:28 pm
>Subject: RE: AMBER: Extended bonds-MD
>
>
>
>>Dear Ananda
>>
>>A few comments on your input options:
>>
>>
>>
>>>MD_simulation of IMB in PBC_1
>>> &cntrl
>>> imin = 0, irest = 0, ntx = 1,
>>> ntt = 1, temp0 = 10.0,
>>>
>>>
>>temp0=10.0 you only want a temperature of 10 kelvin correct?
>>
>>
>>
>>>tautp = 1, gamma_ln = 10000,
>>>
>>>
>>gamma_ln is not used when ntt=1 only with ntt=3. For the record
>>though a
>>value of 10000 for gamma_ln is huge. A value of 4 or 5 would be more
>>appropriate.
>>
>>
>>
>>> ntp = 0,
>>> ntb = 1, ntc = 1, ntf = 7,
>>>
>>>
>>ntf=7 -> This almost certainly the cause of your problems. This
>>means omit
>>all bond angle and dihedral interactions. Do you really want to do
>>this? In
>>my experience running a simulation of a protein with just non-bonded
>>interactions is never stable. The only time I find you can get away
>>withNTF>1 is for NTF=2 and only then when you have shake turned on
>>(ntc=2).Also, since you are running a 0.5fs time step there is
>>nothing to really be
>>gained from ommiting bonds angles and dihedrals. I would treat ntf
>>valuesgreater than 2 as being developer/debugging options.
>>
>>
>>
>>> cut = 20.0,
>>>
>>>
>>20 angstroms is probably much much bigger than you need for a periodic
>>boundary simulation. Set it to 8 angstroms and only increase it if
>>you don't
>>run with PME.
>>
>>
>>
>>>scee = 4.0, scnb = 20.0,
>>>
>>>
>>Why have you changed these? These really are developer options and
>>should"never?" be changed by the end user without good reason. The
>>entire force
>>field (FF99, FF03...) is parameterised around the default values of
>>thesescaling factors. SCNB should be 2.0 and scee should be 1.2.
>>Only change them
>>if you have for some reason built yourself a completely new force
>>field.
>>
>>
>>>keep PIB fixed with strong constraints
>>>100
>>>RES 1 64
>>>END
>>>END
>>>
>>>
>>100.0 KCal/mol is a pretty big restraint and may cause instability
>>in your
>>system. It is probably ok for minimisation but I would reduce this
>>duringmolecular dynamics. A value of 10 or less should be
>>sufficient to keep these
>>residues fixed reasonably close to the initial structure.
>>
>>
>>
>>
>>>is it due to the less simulation time period or the effect of box
>>>
>>>
>>size> or the effect of some other parameters.
>>
>>This is an artifact of the various "strange" options in your input
>>file that
>>I have highlighted above.
>>
>>All the best
>>Ross
>>
>>/\
>>\/
>>|\oss Walker
>>
>>| Department of Molecular Biology TPC15 |
>>| The Scripps Research Institute |
>>| Tel:- +1 858 784 8889 | EMail:- ross_at_rosswalker.co.uk |
>>| http://www.rosswalker.co.uk/ | PGP Key available on request |
>>
>>Note: Electronic Mail is not secure, has no guarantee of delivery,
>>may not
>>be read every day, and should not be used for urgent or sensitive
>>issues.
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>>
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-- 
===================================================================
Carlos L. Simmerling, Ph.D.
Associate 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
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