Hi mark
I think if this was the case i will see the box simply shrink but no change either in density or dipole moment..but what i have seen is that the box enlarges and dipole moment changes..my feeling is that the cubic cell is somehow disfigured..indeed the longer the simulation the less cubic the box...if you have other suggestions please tell...thanks for the paper...
Regards
Marawan
------------------------------
On Mon, Dec 3, 2012 1:14 AM PST Marc van der Kamp wrote:
>PS Sorry, that should be: "water molecules may have a different optimal
>*distance from* your nucleoside"
>--Marc
>
>On 3 December 2012 09:10, Marc van der Kamp <marcvanderkamp.gmail.com>wrote:
>
>> Dear Marawan,
>>
>> I don't know about your specific combination of QM and MM level, but the
>> difference you see between pure MM, DFTB/MM and PBE/MM may originate (in
>> part) from the fact that different QM and MM levels/force-fields will have
>> different optimal Van der Waals (Lennard-Jones) parameters. This could
>> cause a (small) difference in density, as the water molecules may have a
>> different optimal difference form your nucleoside.
>>
>> This paper may be relevant:
>> Pentikainen U, Shaw KE, Senthilkumar K, Woods CJ & Mulholland AJ (2009)
>> Lennard-Jones Parameters for B3LYP/CHARMM27 QM/MM Modeling of Nucleic Acid
>> Bases. Journal of Chemical Theory and Computation 5: 396-410
>>
>> Hope this helps,
>> Marc
>>
>>
>>
>> On 3 December 2012 09:02, marawan hussain <marawanhussain.yahoo.com>wrote:
>>
>> Dear AMBER users,
>> I'm running an NPT QM/MM simulation using the AMBER/ORCA interface using
>> PBE for the QM system. The system is composed of a nucleosde (QM) dissolved
>> in a 20 A water box (MM).The system is equilibrated in the NPT ensemble
>> classically and using also DFTB as implemented in AMBER. I'm using spcfw
>> water model and 0.5 fs time step and no shake..I'm noticing that the dipole
>> moment of the QM region is lowered by time and also the system density. At
>> the first period the dipole moment is more than (10 D) which as i
>> understand a result for the presence of the water molecules which increases
>> the dipole moment. Afterthat, after around 2000 timesteps (almost 1 ps) the
>> dipole moment is decreased and also the density. Density drops from (1.0097
>> to 0.9929 ), also the volume increase a little bit (104011.5218 to
>> ====> 105806.9653). i visualized the trajectory and i didn't find anything
>> problematic. Could you please comment.
>> I'm using periodic boundary conditions. I'm allowing the water molecules
>> flexibility..Below is the input.
>> Regards
>> Marawan
>>
>> system equilibration qm-mm
>> &cntrl
>> imin = 0,
>> ntpr = 1,ntwx = 1, ntwr = 1000,
>> nstlim = 6000,dt = 0.0005,
>> tempi = 300.0, temp0 = 300.0,
>> ntb=2, ntp=1, taup=1,
>> ntr = 0,
>> cut = 15.0, ig=-1,jfastw=4,
>> ntt = 3, gamma_ln = 10.0, ifqnt=1
>> &end
>> &qmmm
>> qmmask=':1'
>> qmcharge=0,
>> qm_theory='EXTERN',
>> qmcut=15.0,
>> qm_ewald=0
>> &end
>> &orc
>> use_template=1,
>> ntpr=1,
>> num_threads=8,
>> dipole=1
>> &end
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>>
>>
>>
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Received on Mon Dec 03 2012 - 04:30:02 PST
