I'm not using Amber myself to speak of, but there's an example of using
nmr restraints to modify the target temperature on this page:
http://ambermd.org/tutorials/advanced/tutorial5_amber9/section5.htm
You will also want to look into gradual relaxation of your restraint.
On 4/12/17 10:41 PM, Jorgen Simonsen wrote:
> Thanks - just to clarify I have followed some of these tutorial on the
> heating( http://ambermd.org/tutorials/advanced/tutorial8/loop7.htm) I am
> not sure how to gradually heat the system then - could u provide a link or
> some key words I would be able to look into? I would like to increase the
> temperature of the system e.g. 50 K for each 10 ps.
>
> So the system might not to well equilibrated af the 100 ps so would you
> recommend me to run additional 100 ps in the NPT before starting to
> initiate the simulations with new seeds?
>
> Thanks
>
>
>
> On Thu, Apr 13, 2017 at 7:15 AM, Bill Ross <ross.cgl.ucsf.edu> wrote:
>
>> I don't see any gradual warming - your first run doesn't slowly heat,
>> and your final run starts with irest=0 so no velocities.
>>
>> Bill
>>
>>
>> On 4/12/17 10:03 PM, Jorgen Simonsen wrote:
>>> Hi all,
>>>
>>> I am having an issue with the temperature after I have slowly heated up
>> the
>>> system:
>>>
>>> 100ps MD with res on protein
>>>
>>> &cntrl
>>>
>>> imin = 0,
>>>
>>> irest = 0,
>>>
>>> ntx = 1,
>>>
>>> ntb = 1,
>>>
>>> cut = 10.0,
>>>
>>> ntr = 1,
>>>
>>> ntc = 2,
>>>
>>> ntf = 2,
>>>
>>> tempi = 0.0,
>>>
>>> temp0 = 300,
>>>
>>> ntt = 3,
>>>
>>> gamma_ln = 1.0,
>>>
>>> nstlim = 50000, dt = 0.002
>>>
>>> ntpr = 5000, ntwx = 5000, ntwr = 5000
>>>
>>> /
>>>
>>> Keep protein fixed with weak restraints
>>>
>>> 50.0
>>>
>>> RES 1 40
>>>
>>> END
>>>
>>> END
>>>
>>>
>>>
>>> I use the sander.MPI
>>>
>>>
>>> mpirun -np 16 ~/amber14/bin/sander.MPI -O -i md_disulfides.in -p
>>> solv.prmtop -c heat.rst -r md.rst
>>>
>>>
>>> with the following md input file:
>>>
>>>
>>> 10ps MD
>>>
>>> &cntrl
>>>
>>> imin = 0, irest = 0, ntx = 1, iwrap=1,
>>>
>>> ntb = 2, pres0 = 1.0, ntp = 1,
>>>
>>> taup = 2.0,ig=-1,
>>>
>>> cut = 10.0, ntr = 0,
>>>
>>> ntc = 2, ntf = 2,
>>>
>>> tempi = 300, temp0 = 300,
>>>
>>> ntt = 3, gamma_ln = 1.0,
>>>
>>> nstlim = 10000000, dt = 0.002,
>>>
>>> ntpr = 5000, ntwx = 5000, ntwr = 5000
>>>
>>> /
>>>
>>> I do want to start from random seeds to get indenpendent runs so I set
>> the
>>> ig=-1 but still I would expect to be close to the equilibrated system.
>>>
>>> but from the first round I get the following error/ warning
>>>
>>>
>>> NSTEP = 0 TIME(PS) = 100.000 TEMP(K) = 440.42 PRESS =
>>> -621.5
>>>
>>> Etot = -19730.8465 EKtot = 8077.7368 EPtot =
>>> -27808.5832
>>>
>>> BOND = 105.8078 ANGLE = 205.4744 DIHED =
>>> 473.4839
>>>
>>> 1-4 NB = 130.7175 1-4 EEL = 2395.4889 VDWAALS =
>>> 3606.5258
>>>
>>> EELEC = -34726.0816 EHBOND = 0.0000 RESTRAINT =
>>> 0.0000
>>>
>>> EKCMT = 2504.5210 VIRIAL = 4159.2641 VOLUME =
>>> 123313.0860
>>>
>>> Density =
>>> 0.7475
>>>
>>> Ewald error estimate: 0.6640E-04
>>>
>>> ------------------------------------------------------------
>> ------------------
>>>
>>> ***** Processor 0
>>>
>>> ***** System must be very inhomogeneous.
>>>
>>> ***** Readjusting recip sizes.
>>>
>>> In this slab, Atoms found: 1415 Allocated: 1412
>>>
>>>
>>> any help appreciated - thanks!
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>
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>>
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Received on Wed Apr 12 2017 - 23:00:03 PDT
