Dear Professor,
I thank you for your kind early reply.
> Dear Vikram,
>
> This could be from a number of issues although the most likely is the
> restraint force. 1000 KCal/mol/A2 is far too strong. What this will do is
> induce very high frequency oscillations in the CA atom which are too fast
> for the 2 fs step of your integrator and hence the system blows up. Do you
> really need to keep CA of residue 1 fixed this tightly?
>
I dont want to allow the protein to move away from centre.It's the reason
why i am using such a strong restrain force.
>
> You might also have issues with your system not being minimised /
> equilibrated properly. How well equilibrated were things from the run from
> which you are restarting this?
>
>
Not yet. This run is as a part of equilibration only.I wish my system
would be at 200.0 atm pressure. I carried out 1 minimization and a
simulated annealing step.The .rst
file was used for this current run,which is NPT run.
> You may also want to reduce the timestep to say 1fs or so to ensure
> better stability.
>
I ran the NPT with dt= 0.001(1 fs) with reduced restrain force
(mentioned in the prev mail)
Still i got the same "deep energetics problem.
I am tryiyn to run the simmulations as per your suggestions.
Thank you.
-vikram
> All the best
> Ross
>
> /\
> \/
> |\oss Walker
>
> | HPC Consultant and Staff Scientist |
> | San Diego Supercomputer Center |
> | Tel: +1 858 822 0854 | EMail:- ross.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.
>
>
> ------------------------------
> *From:* owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] *On
> Behalf Of *sai vikram
> *Sent:* Tuesday, January 02, 2007 09:10
> *To:* amber.scripps.edu
> *Subject:* AMBER: Deep energetics problem
>
>
>
> Hi,
>
> I am trying to do a NPT simulation with a protein structure restraining
>
> Restrain 2 to 20 residues
>
> 1.0
>
> Restrain the CA atom of first residue strongly
>
> 1.0
>
> Before this particular run i carried out a minimization amd Simulated
> annealing step with restrains.
>
> 50.0
> RES 2 20
> Restrain the CA atom of first residue strongly
> 1000.0
>
>
> I wish my system should be at constant pressure 200.0 .
>
>
> *******************************************************************************
>
> Error:
>
> vlimit exceeded for step 6; vmax = 59.1247
>
> Coordinate resetting (SHAKE) cannot be accomplished,
> deviation is too large
> NITER, NIT, LL, I and J are : 0 2 78 140 141
>
> Note: This is usually a symptom of some deeper
> problem with the energetics of the system.
>
>
> *******************************************************************************
>
> I have tried to search in google and read the messages posted previously
> by others, and reduced the restraints as per their suggestions. Yet, i
> could not able to run my system
> $ Can someone please advice me here. below is my input file
>
> Input file is
>
> --------------------------------------------------------------------------------------------------------------------
> &cntrl
> imin = 0, ntx = 7, irest = 1,
> ntpr = 100, ntwx = 500, ntwe = 0, ntwprt=0,
> ntc = 2, ntf = 2,
> nstlim = 50000, dt =0.002,
> tempi=300.0, temp0 = 300.0, ntt =1, tautp =2.0,
> ntb = 2, ntp = 1,taup=0.2, pres0=200.0,
> ntr=1,iwrap=1,cut=10.0
> &end
> Restrain the heavy atoms
> 1.0
> RES 2 20
> END
> Restrain the CA atom of first residue strongly
> 1.0
> FIND
> * CA * *
> SEARCH
> RES 1
> END
> END
>
>
>
> Amber Version : 9
>
>
> Operating System : Linux
>
>
> --------------------------------------------------------------------------------------------------------------
>
> Thanks in advance,
>
> -Vikram
>
>
>
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Received on Sun Jan 07 2007 - 06:07:04 PST
