Hi,
On Mon, Jul 1, 2013 at 8:01 PM, Mary Varughese
<maryvj1985.gmail.com<javascript:;>>
wrote:
> i am used to center and image commands in ptraj for reimaging . should i
> switch to autoimage of cpptraj?
This is what I would recommend. The 'autoimage' command was designed to be
easier to use.
> could u please explain about wrapping artifacts. how can i check it, just
> visualize?
Either that, or an artifact will typically show up as a large spike in an
RMSD calculation.
> Also sir, on doing rms first mass of a dna ligand system;
> rms first mass :1-24.P,O3',O5',C3',C4',C5' time 1.0
> does this command take care of my ligand :25 also.
No. ":1-24" literally means "residues 1 to 24". One thing you can do to see
how residue 25 moves with respect to residues 1-24 is use that initial mask
to perform the initial fit, then do an rms calculation on residue 25 without
fitting, e.g.:
rms first mass :1-24
rms first mass :25 nofit out rms.25.dat
-Dan
> or should i use
> rms first mass :1-24.P,O3',O5',C3',C4',C5' :25 time 1.0
> but this command output says nothing about :25
> how can i now ligand is also rms fitted?
>
>
> On Tue, Jul 2, 2013 at 7:08 AM, David A Case <case.biomaps.rutgers.edu<javascript:;>
>wrote:
>
>> On Mon, Jul 01, 2013, Mary Varughese wrote:
>> >
>> > in the production dynamics(in NPT):
>> > when ntb=2, ntp=1, pres0=1.0, ntt=3
>> >
>> > 1: what should be the appropriate value of gamma_ln ? (i have used 1 )
>> > does increasing value to 5.0 has any advantage
>>
>> I doubt that you could see any difference between 1 and 5.
>>
>> > 2: also what is the significance of taup=2.0 ; how does it affect the
>> > dynamics
>>
>> The affects the speed at which the volume of the system responds to
>> pressure
>> fluctuations, and hence to the magnitude of the fluctuations themselves.
>> If your system is too small (doesn't have enough water molecules) the
>> value
>> of this variable might cause a noticeable difference, although I have not
>> personally seen such a case.
>>
>> > 3: also should i essentiallly include ig=-1 as it says in amber DNA
>> > tutorials in the case of ntt=3.
>>
>> Yes: this is essential.
>>
>> > 4: Also i hope adding these values doesnt affect mmpbsa calculations.
>>
>> Not setting ig=-1 could lead to very bad results. Minor variations in
>> gamma_ln or taup are unlikely to have measurable effets.
>>
>> >
>> > 5: Also sir does iwrap=1 has any influence on mmpbsa calculations?
>>
>> It can. The safest course of action is to use the "autoimage" command in
>> cpptraj before handing things off to mm-pbsa. Also, be sure to visualize
>> your trajectory (after autoimage) to make sure there are no wrapping
>> artifacts.
>>
>> ...dac
>>
>> p.s.: be sure to study reviews of mm-pbsa calculations, and look for
>> papers that report calculations similar to the ones you are planning. In
>> my opinion, a careful study of what happens during your simulation is a
>> lot more likely to lead to new insights than are the energies that come
>> out of the mmpbsa analysis.
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org <javascript:;>
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org <javascript:;>
> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-9119 (Fax)
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-9119 (Fax)
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Jul 01 2013 - 22:00:03 PDT
