Yeah I know, but still there is a qualitatively jump that stays stable for each different 5ns simulation, I attach a figure hope you can see it. Carlos Simmerling explained me what you say that there is jump in time, and restarting I understand also produces some "instantaneous jump in the restraint energy, which changes the forces and the simulation adjusts to a new average structure with different energy” in Carlos words.
But still it puzzled me a little, here is the jump please notice it gets smaller and smaller with simulation time…. but there is a jump specially after 5ns and 10 ns, there it gets much better.
I plan to use your MMPBSA.py script only starting at 20 or 30 ns for 20 ns (2000 frames) is that good enough?
Thanks!!
fabian
Dr. Fabian Glaser
Head of the Structural Bioinformatics section
Bioinformatics Knowledge Unit - BKU
The Lorry I. Lokey Interdisciplinary Center for Life Sciences and Engineering
Technion - Israel Institute of Technology, Haifa 32000, ISRAEL
fglaser at technion dot ac dot il
Tel: +972 4 8293701
http://bku.technion.ac.il
> On 27 Oct 2015, at 6:02 PM, Adrian Roitberg <roitberg.ufl.edu> wrote:
>
> Hi
>
> just to make sure we are all on board, you are NOT comparing the last
> step on MD 1 with the first step of MD 2, but rather the last step of
> MD1 with the 5000th step of MD 2.
>
>
> So, there is no reason why those two values should be the same.
>
> As always, plot total energy vs 'time' and see if there is really a jump
> (as in a large chaneg between MD1 and 2) or just a fluctuation.
>
> adrian
>
>
>
>
> On 10/27/15 10:03 AM, Fabian gmail wrote:
>> Hi thanks for the reply
>>
>> Here is the graph, my input file is the following
>>
>> prod10 DG_mn22 5ns
>> &cntrl
>> imin=0,irest=1,ntx=5,
>> nstlim=2500000,dt=0.002,
>> ntc=2,ntf=2,
>> cut=8.0, ntb=2, ntp=1, taup=2.0,
>> ntpr=5000, ntwx=5000,
>> ntt=3, gamma_ln=2.0,
>> temp0=300.0,
>> ntr=1, restraintmask=':1-704.CA,C,N',
>> restraint_wt=0.5,
>>
>> /
>>
>>
>> this is the las step of the first 5 ns
>>
>> NSTEP = 2500000 TIME(PS) = 5600.000 TEMP(K) = 300.45 PRESS = 18.4
>> Etot = -237462.0603 EKtot = 61305.5273 EPtot = -298767.5876
>> BOND = 2109.8343 ANGLE = 5811.6787 DIHED = 8549.7911
>> 1-4 NB = 2991.7893 1-4 EEL = 44880.8758 VDWAALS = 34038.3809
>> EELEC = -397553.7075 EHBOND = 0.0000 RESTRAINT = 403.7698
>> EAMBER (non-restraint) = -299171.3574
>> EKCMT = 26295.0548 VIRIAL = 25891.9488 VOLUME = 1015249.7295
>> Density = 0.9997
>>
>> And this is the first of next run, using the same input exaxtly and the .rst file you can see the energy is lower….
>>
>> NSTEP = 5000 TIME(PS) = 5610.000 TEMP(K) = 299.99 PRESS = 123.8
>> Etot = -238869.6914 EKtot = 61211.6992 EPtot = -300081.3906
>> BOND = 2207.0869 ANGLE = 5651.6540 DIHED = 8487.2619
>> 1-4 NB = 2978.0329 1-4 EEL = 44929.7915 VDWAALS = 34412.9426
>> EELEC = -398938.7728 EHBOND = 0.0000 RESTRAINT = 190.6124
>> EAMBER (non-restraint) = -300272.0030
>> EKCMT = 26243.7459 VIRIAL = 23549.8423 VOLUME = 1007578.4884
>> Density = 1.0073
>>
>>
>>
>>
>> Dr. Fabian Glaser
>> Head of the Structural Bioinformatics section
>>
>> Bioinformatics Knowledge Unit - BKU
>> The Lorry I. Lokey Interdisciplinary Center for Life Sciences and Engineering
>> Technion - Israel Institute of Technology, Haifa 32000, ISRAEL
>>
>> fglaser at technion dot ac dot il
>> Tel: +972 4 8293701
>> http://bku.technion.ac.il
>>
>>
>>> On 27 Oct 2015, at 3:56 PM, Carlos Simmerling <carlos.simmerling.gmail.com> wrote:
>>>
>>> I didn't get an attachment, but it might help if you put in the email text
>>> your input file for the run that showed the energy jump as well as the step
>>> right before it.
>>>
>>> On Tue, Oct 27, 2015 at 9:36 AM, Fabian gmail <fabian.glaser.gmail.com>
>>> wrote:
>>>
>>>> Hi,
>>>>
>>>> When running several simulations of the same protein, 5ns each, there is a
>>>> small jump in energy when starting the next one (which uses of course the .
>>>> rst file of the previous one as the starting point), why is that???
>>>>
>>>> Here is the graph of energy vs time, the jump is at time 5600 (since the
>>>> equil was 600 ps). Why?
>>>>
>>>> Thansk a lot,
>>>>
>>>> Fabian
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> Dr. Fabian Glaser
>>>> Head of the Structural Bioinformatics section
>>>>
>>>> Bioinformatics Knowledge Unit - BKU
>>>> The Lorry I. Lokey Interdisciplinary Center for Life Sciences and
>>>> Engineering
>>>> Technion - Israel Institute of Technology, Haifa 32000, ISRAEL
>>>>
>>>> fglaser at technion dot ac dot il
>>>> Tel: +972 4 8293701
>>>> http://bku.technion.ac.il
>>>>
>>>>
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>
> --
> Dr. Adrian E. Roitberg
> Professor.
> Department of Chemistry
> University of Florida
> roitberg.ufl.edu
> 352-392-6972
>
>
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Received on Tue Oct 27 2015 - 09:30:04 PDT
