Hi Chunhu,
What did you use for the reference structure?
When running NPT dynamics the box size gets scaled as do residue positions.
This means that if you restrain to the initial starting structure you will
often get huge restraint forces and vlimit errors.
When running NPT I typically use the following protocol:
1) -O -i mdin.1 -o mdout.1 -p prmtop -c inpcrd -r restart.1 -refc inpcrd
2) -O -i mdin.2 -o mdout.2 -p prmtop -c restart.1 -r restart.2 -refc
restart.1
3) -O -i mdin.3 -o mdout.3 -p prmtop -c restart.2 -r restart.3 -refc
restart.2
That is you always restrain to the current input coordinates for this run
rather than to the starting coordinates. This is a function of the way
things work for pressure scaling when one has restraints on. If you use
constant volume it should not be a problem to always restrain to the initial
starting structure. You have to think that using constant pressure with
restraints is not going to be strictly correct in that when you scale the
positions to adjust the pressure you run into problems with the restrained
part. If you are just restraining things to allow part of the system to
relax independently from another part then the above protocol should be
sufficient.
All the best
Ross
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> -----Original Message-----
> From: owner-amber.scripps.edu
> [mailto:owner-amber.scripps.edu] On Behalf Of Chunhu Tan
> Sent: Monday, September 18, 2006 10:47
> To: amber.scripps.edu
> Subject: AMBER: Restart problem on PMEMD with position restraint.
>
>
> Hi, All,
>
> I got a Vlimit error when I wanted to restart a PMEMD
> simulation with
> position restraint. My system is protein G solvated in a
> TIP3P water box
> with 11 angstroms buffer. After the minimization, I first run 20ps NVT
> simulation, then 20ps NPT simulation. All these were OK, but when I
> wanted to restart the NPT simulation, I got the Vlimit error, even I
> used exact the same input file as the first NPT run.
> I am using AMBER9, and here are the inputs:
>
> 1) MD_NVT.IN
> &cntrl
> imin = 0,
> irest = 0, ntx = 1,
> ntb = 1,
> ntt = 3, gamma_ln =1.0,
> iwrap = 1,
> ntf = 2, ntc = 2, tol = 0.000001,
> temp0 = 300, tempi = 300,
> nstlim= 10000,
> ntpr = 1000, ntwr = 1000, ntwx = 10000,
> dt = 0.002,
> cut = 9,
> ntr = 1
> /
> &ewald
> skinnb = 1.
> /
> Hold the protein fixed
> 50.0
> RES 1 56
> END
>
> _______________________________________
> 2) MD_NPT.IN
> &cntrl
> imin = 0,
> irest = 1, ntx = 5,
> ntb = 2, ntp = 1,
> ntt = 1, iwrap = 1,
> ntf = 2, ntc = 2, tol = 0.000001,
> temp0 = 300,
> nstlim= 10000,
> ntpr = 5000, ntwr = 5000, ntwx = 200000,
> dt = 0.002,
> cut = 9,
> ntr = 1
> /
> &ewald
> skinnb = 1.
> /
> Hold the nucleic acid fixed
> 50
> RES 1 56
> END
> END
>
>
> --------------------------------------------------------------
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Received on Wed Sep 20 2006 - 06:07:11 PDT
