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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>>
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Received on Tue Oct 27 2015 - 07:30:05 PDT
