Re: [AMBER] STOP PMEMD Terminated Abnormally!

From: Pragya Priyadarshini <>
Date: Mon, 17 Aug 2015 19:54:53 +0530


Thanks for the reply.

Since I am using same input file that I have prepared earlier for
Amber11 where ioutfm=1 was for netCDF trajectory so I have used this
only. I did not use ntxo=2 this time.

So I want to be clear that, will this affect my MD run for 1-50 ns where
i have used only ioutfm not ntxo?


On 2015-08-17 17:21, David A Case wrote:

> On Mon, Aug 17, 2015, Pragya Priyadarshini wrote:
>> I am doing MD simulation of Protein-DNA complex for total 80 ns. I have been using iwrap=0 for all the production run and it worked fine till 50ns . while extending simulation run after 50ns it is unable to read restart file. By the help of Amber mailing list I came to know that for long run MD simulation iwrap=1 should be use. Now I am running MD with iwrap=1, though it is reading the restart file I am concerned that if it could affect the calculation during next MD run.
> What you describe should be fine. But we recommend using netCDF format for
> both restart and trajectory files: set ioutfm=1 and ntxo=2.
> ...dac
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> AMBER mailing list
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Pragya Priyadarshini
Junior Research Fellow
C/o Dr. Balvinder Singh
Bioinformatics Center (G N R P C)
Institute of Microbial Technology-CSIR
Sector 39A, Chandigarh-160036, INDIA
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Received on Mon Aug 17 2015 - 07:30:04 PDT
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