Dear AMBER users,
It is basic question, but I can’t figure out
I am trying to simulate DNA only of my system, the simulation box 20 A as in photo no.1
Then Minimization finished by only 26000 steps, Although I adjusted to 200 000 steps. In photo no 2
I already looked for this strange ending of minimization, but old messages of Amber list said it's okay.
Then run NVT ( retrained all heavy atoms with force 10) and it’s finished normally and the trajectory okay, also I checked the RMSD photo no.3
After that, I tried to run NPT with restrain 10 as a first step then I will reduce gradually, however couldn’t run the error message photo no. 4
So, Do u have any suggestion to solve this problem?
Best regards,
Mohamed Marzouk Sobeh
Ph.D student at Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan.
T.A Physics department,Ain Shams University, Cairo, Egypt.
Emails:
mohamed_marzouk.sci.asu.edu.eg
marzouk.aa.m.titech.ac.jp
marzouk_biophysics.yahoo.com
mohamedmarzoukphysics.gmail.com
Mob. and WhatsApp.:
+81 070-4070-9549
+2 01061417414
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Received on Wed Oct 07 2020 - 07:30:02 PDT
