Hi Santosh,
On 28/10/2010, at 8:17 a.m., Santosh Mogurampelly wrote:
> Dear Amber,
> I am doing a simulation of RNA with NaCl salt. I am able to do MD without
> fail for 100mM, 200mM and 500mM but when I increase the salt to 1000mM,
> the simulations fails in the initial stage. SANDER output says:
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 1 NaN NaN 1.9954E+12 Cl- 1079
>
> BOND = 109.1329 ANGLE = 941.2407 DIHED =
> 529.7401
> VDWAALS = NaN EEL = NaN HBOND =
> 0.0000
> 1-4 VDW = 518.6927 1-4 EEL = -1686.6642 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 100 NaN NaN 0.0000E+00 P 1
>
> BOND = NaN ANGLE = 101106.7185 DIHED =
> 353.8000
> VDWAALS = -1004.0093 EEL = NaN HBOND =
> 0.0000
> 1-4 VDW = NaN 1-4 EEL = NaN RESTRAINT = NaN
> EAMBER = NaN
>
> the initial structure looks fine and inputs are all correct. This problem
> is arising only when I increase NaCl concentration to 1000mM. Any
> suggestion/help would be highly appreciated.
This output suggests to me that you have two atoms, one of which is Cl 1079,
on top of, or at least very close to, each other.
Before starting, did you run the "check" command in LeAP? It takes a while,
but it would point out any close contacts in your system. If atoms really are
virtually on top of each other (say, within 0.2 Å), you can sometimes have
problems, and you may need to move one of the atoms by a small distance
before starting.
Given that your output contains references to RMS and GMAX, I'm guessing that
this output is from a minimisation. If so, a good procedure is to start with
a number of steepest-descent steps before switching to another algorithm such
as conjugate gradients. The default operation is to do only 10 steps of
steepest descents, which may not be sufficient. You could try increasing this
using the "ncyc" option in your mdin file. ncyc=100 might be a good place to
start.
Another thing that may help you in your troubleshooting is to increase the
frequency of energy outputs to the mdout file. During minimisations, I
typically report energies at every step (i.e., ntpr=1 in your mdin file).
This helps to track down what's happening with the energies, such as whether
they really are going down, and what atoms might have the worst problems.
Hope that helps,
Ben
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Received on Thu Oct 28 2010 - 06:30:02 PDT
