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!
>>>>> _______________________________________________
>>>>> AMBER mailing list
>>>>> AMBER.ambermd.org
>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>> _______________________________________________
>>>> AMBER mailing list
>>>> AMBER.ambermd.org
>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Apr 13 2017 - 00:00:02 PDT
