Hi,
I would advise you to do one heating step and one equilibration step before the production runs.
These absolute numbers of potential energies and EGB, I believe, have no meaning per se unless you comparing with another system which was simulated under identical conditions. These numbers are large because they are sum of your force field terms and for a protein with several thousand atoms this sum is likely to be a large number.
Best Regards
Elvis Martis
Ph.D. Student (Computational Chemistry)
at Bombay College of Pharmacy
A Kalina, Santacruz [E], Mumbai 400098, INDIA
W www.elvismartis.in
Skype. adrian_elvis12
-----Original Message-----
From: Ramin Salimi [mailto:ramin.salimi01.utrgv.edu]
Sent: Saturday, May 13, 2017 7:14 PM
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] error: At line 551 of file mdin_ctrl_dat.F90 (unit = 5, file = 'heat.mdin')
Hi Elvis
Thanks so much for correcting the syntax error.
I also would like to ask when we are running implicit solvation, how many steps are needed for heating, and equilibration phases? Is it better to do them in only one step because there is no water molecule or we should do the heating and equilibration in more than one step?
The other question I have is that when it shows in the .mdout file that the potential energy and EGB are negative of the order 10^4, what does this mean? why so much big a number when it is being done in implicit solvation method?
Thanks
Ramin
________________________________
From: Elvis Martis <elvis.martis.bcp.edu.in>
Sent: Saturday, May 13, 2017 8:21:00 AM
To: AMBER Mailing List
Subject: Re: [AMBER] error: At line 551 of file mdin_ctrl_dat.F90 (unit = 5, file = 'heat.mdin')
Sorry, there was one more correction in your input file. please see use the input file attached here.
Best Regards
[photo]
Elvis Martis
Ph.D. Student (Computational Chemistry)
at Bombay College of Pharmacy
A Kalina, Santacruz [E], Mumbai 400098, INDIA W
https://na01.safelinks.protection.outlook.com/?url=www.elvismartis.in&data=02%7C01%7Cramin.salimi01%40utrgv.edu%7C6733723cd2aa4856548208d49a02ec48%7C990436a687df491c91249afa91f88827%7C0%7C0%7C636302784754145935&sdata=h1qKV7J5BBzJp%2FVAqUIsvvAxuqsTxuhAkFfW5XKyvfg%3D&reserved=0<
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________________________________
From: Ramin Salimi <ramin.salimi01.utrgv.edu>
Sent: 13 May 2017 17:51:35
To: amber.ambermd.org
Subject: [AMBER] error: At line 551 of file mdin_ctrl_dat.F90 (unit = 5, file = 'heat.mdin')
Dear Amber users
I am running implicit solvation simulation, and now wanna heat up the system. But I get the following error:
At line 551 of file mdin_ctrl_dat.F90 (unit = 5, file = 'heat.mdin')
This is my input file(heat.mdin):
&ctrl
imin=0, irest=0, ntx=1,
nstlim=300000, dt=0.002,
ntc=2, ntf=2, ioutfm=1, ig=-1,
ntt=3, gamma_ln=5.0,
tempi=100.0, temp0=300.0,
ntpr=100, ntwx=100, ntwr=100
ntb=0, igb=8, gbsa=1,
cut=999.,rgbmax=999.
/
I think the input file looks fine but I cannot figure out what the error goes back to? In the mdout file it does not type any comment on the error, and it just shows the input parameters. Also the parameter file is attached.
I would appreciate if you help me figure this out
Thanks
Ramin
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Received on Sat May 13 2017 - 08:00:02 PDT
