On Tue, Nov 28, 2017, Rana Rehan Khalid wrote:
>
> I want to minimize the structure but when simulation start the values of
> VDWAALS not show. is it due to poor starting structure or structure have
> more clashes. KIndly tell hoe i can remove the clashes through MD
> simulation. Regards
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 1 3.3484E+18 9.6235E+17 4.9465E+20 C 6484
>
> BOND = 5320.4918 ANGLE = 24456.6551 DIHED =
> 20708.3171
> VDWAALS = ************* EEL = -645997.9707 HBOND =
> 0.0000
> 1-4 VDW = ************* 1-4 EEL = 56119.7849 RESTRAINT =
> 0.0000
You have two atoms almost of top of one another. (The "****" means
the number is too big to fit in the space provided.) You can use the
"checkoverlap" command in cpptraj to locate these.
If there only a small number of such clashes, minimization will often solve
the problem: try 100 steps of minimization, and print at every step (ntpr=1).
If you are lucky, you will arrive at a useful structure. If not, you will
have to figure out a way to get a better starting structure.
....dac
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Received on Tue Nov 28 2017 - 06:00:04 PST
