I.e. I haven't heard of a definitive answer. I would think that once
equilibrium density has been achieved, variation might not be important,
and pressure scaling has its own issues, which counseling can help with
perhaps, but maybe validly avoided.
On 4/12/17 11:44 PM, Bill Ross wrote:
> I'm more following what I perceive the crowd to be doing on that, since
> I haven't run anything with water in a decade.
>
>
> On 4/12/17 11:10 PM, Jorgen Simonsen wrote:
>> well I will have to end up in the NPT though - your reason for NVT is that
>> speed?
>>
>> On Thu, Apr 13, 2017 at 7:57 AM, Bill Ross <ross.cgl.ucsf.edu> wrote:
>>
>>> Normally I'd run NPT until volume equilibrates as a first step towards a
>>> starting ensemble, see the literature for what people call equilibrated
>>> these days. Once volume has equilibrated, you can switch to NVT.
>>>
>>>
>>> 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!
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Received on Thu Apr 13 2017 - 00:00:03 PDT
