Hi Vero,
Thank you for the detailed response!
first the minimization and then the equilibration step
Usually there’s one or more steps between the minimization and the restraint-free NPT equilibration. The purpose is gradually heating (to bring up the temperature of) the system and pressing (to achieve a relatively realistic density). During these steps, you can apply restraints on the solute or important parts of the system to prevent drastic changes of structure.
I asked similar questions on the list server before, and other experts told me to be gentle to the structures when performing alchemical simulations. If you can get regular MD simulations running for your system, likely you have these steps before the final production run. I designed my TI protocol based on the regular MD protocol I have been using for my system, and it worked for majority of the lambda states.
Hope this helps!
Bests,
Amy
From: VERONICA MARTIN HERNANDEZ <veronica.martin.hernandez.uva.es>
Date: Thursday, March 21, 2024 at 11:18 AM
To: He, Amy <he.1768.buckeyemail.osu.edu>, AMBER Mailing List <amber.ambermd.org>, dacase1.gmail.com <dacase1.gmail.com>
Subject: RE: [AMBER] [Sender Not Verified] Re: AMBER error vlimit exceed for step
Hi Amy I was inspecting the input files of the TI and I've got a question. This is my input file of a minimization: minimisation &cntrl imin = 1, ntmin = 2, maxcyc = 1000000, ntpr = 500, ntwe = 20, dx0 = 1. 0D-7, ntb = 1, ntxo = 1, icfe
Hi Amy
I was inspecting the input files of the TI and I've got a question.
This is my input file of a minimization:
minimisation
&cntrl
imin = 1, ntmin = 2, maxcyc = 1000000,
ntpr = 500, ntwe = 20,
dx0 = 1.0D-7,
ntb = 1,
ntxo = 1,
icfe = 1, ifsc = 1, clambda = 0.5, scalpha = 0.5, scbeta = 12.0,
logdvdl = 0,
timask1 = ':408', timask2 = ':409',
scmask1 = '.6559, 6562', scmask2 = '.6588, 6591',
/
&ewald
/
And this the equilibration input file:
TI equilibration
&cntrl
imin = 0,
nstlim = 200000,
irest = 0,
ntx = 1,
dt = 0.001,
ntt = 3,
temp0 = 300.0,
gamma_ln = 2.0,
ig = -1,
ntc = 1,
ntf = 1,
ntb = 2, ntp = 1, pres0 = 1.01325, taup = 2.0, barostat = 2 !constant preasure regulated by montecarlo barostat
ntwe = 100,
ntwx = 100,
ntpr = 100,
ntwr = 100,
icfe = 1, ifsc = 1, clambda = 0.5, scalpha = 0.5, scbeta = 12.0,
logdvdl = 0,
timask1 = ':408', timask2 = ':409',
scmask1 = '.6559, 6562', scmask2 = '.6588, 6591',
/
&ewald
/
maybe because the equilibration has the command gamma_ln and the minimization doesn't have it, the structure that I have obtained from the minimization isn't correct?? Or there is another thing that makes my system collapses
Thanks in advance
Vero
________________________________
De: He, Amy <he.1768.buckeyemail.osu.edu>
Enviado: miércoles, 20 de marzo de 2024 20:21
Para: VERONICA MARTIN HERNANDEZ <veronica.martin.hernandez.uva.es>; AMBER Mailing List <amber.ambermd.org>
Asunto: Re: [AMBER] [Sender Not Verified] Re: AMBER error vlimit exceed for step
Hi Vero,
Not sure this helps, but besides energies, have you looked at other physical properties, such as temperature and density, in the steps before you encountered the vlimit exceed error?
What other types of simulations did you run between minimization and the restraint-free (?) NPT equilibrium, and how did they go?
If you can’t post on the list server, having someone you trust or within your institution to look at details of your simulations might help.
--
Amy He
Hadad Lab . OSU
He.1768.osu.edu
From: VERONICA MARTIN HERNANDEZ via AMBER <amber.ambermd.org>
Date: Wednesday, March 20, 2024 at 2:07 PM
To: David A Case <dacase1.gmail.com>, AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] [Sender Not Verified] Re: AMBER error vlimit exceed for step
Hi
Thanks for the advice. I have performed the autoimage command, and I see how the system blows up
I have also put the input of nstlim=0 but I've got an error and the calculation doesn't start, there is an error mcbarint. Due to that error, I have tried to put nstlim=200, and save every step and there is a point where the temperature increases like 10000 K
So, now, I don't know what is happening in my system
Thanks for all the help and I hope I have explained it well
Best regards
Vero
________________________________
De: David A Case <dacase1.gmail.com>
Enviado: miércoles, 20 de marzo de 2024 15:29
Para: VERONICA MARTIN HERNANDEZ <veronica.martin.hernandez.uva.es>; AMBER Mailing List <amber.ambermd.org>
Asunto: Re: [AMBER] [Sender Not Verified] Re: AMBER error vlimit exceed for step
On Mon, Mar 18, 2024, VERONICA MARTIN HERNANDEZ via AMBER wrote:
>
>Thanks for the advice, I am seeing the problem: the water box
>desintegrates, it's like a water leak in a glass.
Have you run the cpptraj "autoimage" command before doing the visualization?
What you describe sounds like a common problem.
I am still not sure why you seem to be unwilling to set nstlim=0, and then
to examine carefully the energy output from the initial step, comparing it
to the final step of minimization.
...hope this helps....dac
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Received on Thu Mar 21 2024 - 16:30:02 PDT
