Thank you for all suggestions!
I am new in this field and so your detailed answer is really helpful.
I have another short question about the following suggestion:
"You can follow this phase with a few minimizations in which you
gradually relax the restraints (e.g. 2.0 to 0.1 to nothing). Then you
can switch to NPT with restraints on again (at this point 1.0 kcal/mol
Ang^2 is probably fine); use several short (5-10 ps) runs in which you
again gradually relax the restraints. Keep a 1 fs timestep throughout."
Is there a way to set in a single input file all parameters for minimizations in which restraints are gradually relax from e.g. 2.o to 0.0? (or should I have an input file for each minimization?)
Thanks a lot.
Valentina
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Valentina Romano | PhD Student | Biozentrum, University of Basel & SIB Swiss Institute of Bioinformatics
Klingelbergstrasse 61 | CH-4056 Basel |
Phone: +41 61 267 15 80
________________________________________
From: Daniel Roe [daniel.r.roe.gmail.com]
Sent: Thursday, May 08, 2014 7:10 PM
To: AMBER Mailing List
Subject: Re: [AMBER] Analysis of minimization stage
On Thu, May 8, 2014 at 10:32 AM, Valentina Romano
<valentina.romano.unibas.ch> wrote:
> cut=12,
This cutoff might be unnecessarily large for PME. You can probably use
10 or even 8.
> tempi=0.0,
> temp0=300.0,
I am not a huge fan of heating up from 0 K (unless that is what you
specifically need to study for some reason). I feel that assigning
random velocities is much better, otherwise you're really asking a lot
from the thermostat - especially here where you're essentially asking
for an instant jump from 0 to 300 K. I have never had a problem with
assigning random velocities at the temperature of interest (in this
case you would want tempi=300). Make sure you also set ig=-1 (this is
good advice for MD in general unless you need to specifically
reproduce some result).
> ntt=3,
> gamma_ln=1.0,
My personal preference for equilibration is to use the Berendsen
thermostat with tight coupling (ntt=1, tautp=0.5), but Langevin may be
OK as well (although I would increase your gamma_ln to at least 5, and
maybe higher).
> nstlim=50000, dt=0.002,
This is probably longer than you need for this stage, and as was
previously suggested definitely use a 1 fs timestep.
> ntpr=100, ntwx=100, ntwr=1000
> restraint_wt = 1.0,
> restraintmask=':1-247.CA,C,O,N'
I like a stronger restraint initially (5 kcal/mol Ang^2), which can be
gradually relaxed in subsequent phases.
You can follow this phase with a few minimizations in which you
gradually relax the restraints (e.g. 2.0 to 0.1 to nothing). Then you
can switch to NPT with restraints on again (at this point 1.0 kcal/mol
Ang^2 is probably fine); use several short (5-10 ps) runs in which you
again gradually relax the restraints. Keep a 1 fs timestep throughout.
When you finally have all restraints off be sure to monitor your
system density - when that stops changing significantly your system
should be in decent shape.
Hope this helps,
-Dan
>
>
> Do you have specif suggestion about it?
>
> -Valentina
>
>
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> Valentina Romano | PhD Student | Biozentrum, University of Basel & SIB Swiss Institute of Bioinformatics
> Klingelbergstrasse 61 | CH-4056 Basel |
>
> Phone: +41 61 267 15 80
>
>
> ________________________________________
> From: Daniel Roe [daniel.r.roe.gmail.com]
> Sent: Thursday, May 08, 2014 6:21 PM
> To: AMBER Mailing List
> Subject: Re: [AMBER] Analysis of minimization stage
>
> Hi,
>
> On Thu, May 8, 2014 at 10:04 AM, Valentina Romano
> <valentina.romano.unibas.ch> wrote:
>> First of all, I minimized the system in 2 steps.
>> 1) only solute restrained
>> 2) all atoms free
>> The input file for the 2nd step is:
>>
>> &cntrl
>> imin=1,
>> maxcyc=10000,
>> ncyc=2500,
>> ntb=1,
>> igb=0,
>> cut=12
>> /
>
> You don't say what input you used for the MD stage, but explicit
> solvent simulations in general require more careful minimization than
> implicit solvent sims. For example, what I usually do is after an
> initial minimization with relatively strong positional restraints on
> solute heavy atoms, my second stage will be a short (15 ps) NVT MD
> simulation with the same restraints using a 1 fs timestep to let the
> water relax, followed by more minimization with gradually decreasing
> restraints. I then switch to a series of short NPT simulations with
> gradually decreasing restraints on solute to allow the density to
> start to equilibrate. If you post your actual MD input we could make
> more specific recommendations.
>
>> I think the error is related to the minimized structure I am using as input.
>> Is there a way to check if the minimization went well (e.g.: an easy way to plot the total energy vs time steps)?
>> How to check if it necessary minimize for a longer or shorter time?
>
> I think that MdoutAnalyzer.py will let you plot energy terms from
> MDOUT output relatively easily. Alternatively you could read MDOUT
> data in with cpptraj (i.e. 'readdata <mdout>'), then write whatever
> terms you want to the file format of your choice with 'writedata'. In
> general you want to pay attention to your gradient - if it's not
> relatively flat for your last steps you probably could do with
> additional minimization. Alternatively you may want to try using the
> XMIN minimizer in sander (ntmin = 3).
>
> Good luck,
>
> -Dan
>
>>
>> The last step of the minimization is the following:
>>
>> NSTEP ENERGY RMS GMAX NAME NUMBER
>> 10000 -1.0588E+05 6.6968E-01 7.0286E+01 N9 3834
>>
>> BOND = 7509.5321 ANGLE = 683.5019 DIHED = 2272.1178
>> VDWAALS = 17150.2089 EEL = -143037.0880 HBOND = 0.0000
>> 1-4 VDW = 785.8019 1-4 EEL = 8760.7170 RESTRAINT = 0.0000
>>
>> While the enrgy at the step 0 of the MD is:
>> NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS = 0.0
>> Etot = -113244.2583 EKtot = 0.0000 EPtot = -113244.2583
>>
>> Could the difference in the energy values had influenced the error I got? If yes, I can solve it?
>>
>> Thank you
>> Valentina
>> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>> Valentina Romano | PhD Student | Biozentrum, University of Basel & SIB Swiss Institute of Bioinformatics
>> Klingelbergstrasse 61 | CH-4056 Basel |
>>
>> Phone: +41 61 267 15 80
>>
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 201
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-6208 (Fax)
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
> AMBER mailing list
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> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Fri May 09 2014 - 02:00:02 PDT
