Sathyaseelan,
did you use iwrap=1 in your MD input?
Maybe your problem can then be resolved by 'unwrapping' your structure
(-> cpptraj command unwrap). Afterwards, you may center your system.
Ensure that you apply the strip commands before the unwrap command;
otherwise all water molecules will be unwrapped as well, which consumes
a lot of CPU resources.
Maybe this helps.
Best,
Anselm
Bioinformatik | NHR.FAU
Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU)
Germany
Am 06.04.2022 um 10:06 schrieb Sathyaseelan C:
> Dear Amber users,
>
>
>
> I am facing an imaging issue during the MD simulation of a
> DNA duplex with trivalent cations. The maging issue happens throughout the
> simulation due to the terminal dimer of one of the DNA strands as well as
> some of the trivalent ions. For instance, in one step the DNA dimer is out
> of the box (as a fragment), but, in the next step it comes back to the
> periodic box and becomes part of the duplex. This happens throughout the
> simulation. I tried with imaging options as below, but, were not useful.
> Any suggestion is highly appreciated.
>
>
>
>
> *For RMSD*
>
>
>
> *1) **Using Image option*
>
> parm prmtop
>
> trajin trajin.nc
>
> reference ../../input/prmcrd
>
> center origin :1-32 # DNA residues
>
> image origin center
>
> center origin :33-44 # trivalent cations
>
> image origin center
>
> strip :WAT
>
> strip :LA
>
> strip :CL
>
> trajout test.pdb pdb
>
> go
>
>
>
> *2) **Using Autoimage option*
>
>
>
> parm prmtop
>
> trajin trajin.nc
>
> reference ../../input/prmcrd
>
> autoimage
>
> strip :WAT
>
> strip :LA
>
> strip :CL
>
> trajout test.pdb pdb
>
> go
>
>
>
>
>
>
>
> Thanks in advance
>
> Sathyaseelan
>
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Received on Wed Apr 06 2022 - 07:00:02 PDT
