Hi
When we do this, for a simple bond breaking/forming, we tend to use
windows roughly 0.1 apart, and force constants of the order of 200.
See like the overlap is better than before, but I would have more
windows between the ones you have now. Try also much larger force
constant around your transition state, which is probably around a value
of zero for your generalized coordinate.
Adrian
On 10/27/15 8:05 AM, Mahmood Jasim wrote:
> Hi Adrian,
>
> Many thanks for your comments; they were very useful. Regarding ig==-1, I
> am using it except in the single input file I copied in the email. I am now
> running the simulation using the generalized distance coordinate as the
> difference between the lenghths of the bond to be formed and the one to be
> broken with 0.2 A windows. This is my restraint file:
>
> iat=1937,6803,6803,6798, r1=-10.0, r2=1.5, r3=1.5, r4=10.0, rstwt=1,-1,
> rk2=50, rk3=50,
>
> and the overlap has greatly improved. The problem starts to happen when the
> coordinate gets closer to the formation of the bond where a big gap appears
> in the graph and the coordinate jumps from 0.15 to -0.3 A. I tried
> increasing the force near the region but it did not work. This is how the
> reaction coordinate versus time looks like:
>
> [image: Inline images 2]
>
> Any advice please
>
> Best Regards,
> Mahmood
>
> On 23 October 2015 at 14:39, Adrian Roitberg <roitberg.ufl.edu> wrote:
>
>> Hi
>>
>> Several comments.
>>
>> Never run the WHOLE set of simulations before you are satisfied with the
>> overlap. Just run 3 or 4 windows and then see if you need to change
>> something before going further.
>>
>> As for your qeustions:
>>
>> Is that sufficient overlap? If it is not, do I need to reduce the spacing
>> or increase the force constant to get better overlap?
>>
>> You do not show the overlap, so it is hard to tell you, but my guess
>> from your first figure is that no, it is not enough. By the way, if you
>> want to increase overlap, you need either a closer spacing and/or a
>> LOWER force constant(not increased!).
>>
>> PLEASE add ig=-1 to your mdin !
>>
>> As for your coordinate, it is NEVER a good idea to use just one distance
>> for a reaction. Look at published work on this, and you will see that
>> peopel tend to use a reaction coordinate that has RC=distance(bond being
>> broken) - distance(bond being made)
>>
>> That produced much more stable surfaces.
>>
>> adrian
>>
>>
>>
>> On 10/23/15 7:56 AM, Mahmood Jasim wrote:
>>> Hi AMBER users,
>>>
>>> I am trying to simulate a reaction involving the formation of a covalent
>>> bond using umbrella sampling combine with QM treatment of the reaction
>>> atoms. I have the SG atom of a cysteine residue attacking an electrophilc
>>> carbon on a ligand. The distance between these 2 atoms is the reaction
>>> coordinate. The windows of umbrella sampling are spaced 0.3 Angstrom
>> apart.
>>> The restraint file looks like this:
>>>
>>> #
>>> # 123 CYM SG 432 UNK C1 3.43
>>> &rst
>>> ixpk= 0, nxpk= 0, iat=1937,6803, r1= 2.93, r2= 3.43, r3= 3.43, r4=
>> 3.93,
>>> rk2=0.0, rk3=100.0, ir6=1, ialtd=0,
>>> &end
>>>
>>> and the md.in file looks like this:
>>>
>>> &cntrl
>>> imin = 0,
>>> irest = 1,
>>> ntx = 7,
>>> ntb = 2,
>>> cut = 12,
>>> ntr = 0,
>>> ntc = 1,
>>> ntf = 1,
>>> igb = 0
>>> ntp = 1
>>> tempi = 300.0,
>>> temp0 = 300.0,
>>> ntt = 3,
>>> gamma_ln = 1.0,
>>> nstlim =10000, dt = 0.001
>>> ntpr = 1000, ntwx = 1000, ntwr = 1000, nmropt = 1,
>>> ifqnt=1,
>>> /
>>>
>>>
>>> &qmmm
>>>
>>> qmmask =
>>> '.1934-1937,6794-6848',
>>> qmcharge =
>>> 0,
>>> qm_theory =
>>> 'PM3',
>>> qmcut =
>>> 12.0,
>>> /
>>> &wt type='DUMPFREQ', istep1=100,/
>>> &wt type='END' /
>>> DISANG=RST-1.dist
>>> LISTOUT=POUT
>>> DUMPAVE=DIST_1.dat
>>>
>>> The run was able to simulate the formation of the bond at the end and the
>>> next graph represents the values of the coordinates across the windows.
>>> [image: Inline images 1]
>>>
>>> Is that sufficient overlap? If it is not, do I need to reduce the spacing
>>> or increase the force constant to get better overlap?
>>>
>>> I used the WHAM code by Alan Grossfieldto calculate PMF with this
>> command:
>>> wham 1.59 3.73 70 0.00001 300 0 meta.dat result.dat
>>>
>>> and this was the meta.dat file:
>>>
>>> DIST_1.dat 3.43 200
>>> DIST_2.dat 3.13 200
>>> DIST_3.dat 2.83 200
>>> DIST_4.dat 2.53 200
>>> DIST_5.dat 2.23 200
>>> DIST_5.dat 1.93 200
>>> DIST_7.dat 1.63 200
>>>
>>> and the histogram I am getting looks like:
>>>
>>> [image: Inline images 2]
>>>
>>> I was expecting the histogram to look different, the PMF to go higher and
>>> then decreases as it approcahes the products. If I managed to improve the
>>> overlapping, will this change the histogrm?
>>>
>>> Many thanks,
>>> Mahmood Jasim
>>> Aston University
>>> UK
>>>
>>>
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>> --
>> Dr. Adrian E. Roitberg
>> Professor.
>> Department of Chemistry
>> University of Florida
>> roitberg.ufl.edu
>> 352-392-6972
>>
>> _______________________________________________
>> 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
--
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 - 06:00:04 PDT
