On Wed, 2014-09-10 at 15:06 +0000, Kong, Ren wrote:
> Hi all,
>
> I ran a 4 ns MD simulation and did the RMSD analysis. I found a few frames having very large RMSD, such as 27.4 Å while the others were normal (~3 Å).
> I thought it would be the discontinued trajectory problem as I used IWRP=1 in MD input file.
> Then I used following commands in order to map the frames to the original cell according to the AmberTools manual:
>
> trajin ../../macro_prod1.nc 3000 4000
> trajout macro_prod1_noWAT2.mdcrd
> unwrap :1-259 ### 1-259 is the number of residues of the protein in my simulation system.
This is a pointless command, since you promptly try to reverse it the
very next step.
> center :1-259 mass origin
> image center origin familiar
Try replacing these two commands with "autoimage" (make sure you're
using cpptraj).
> strip :WAT,Na+
> go
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Wed Sep 10 2014 - 09:00:02 PDT
