Hi,
Sorry, I attached an old file that was obviously wrong for the reasons you just mentioned. I fixed it, and this is my new file.
NRB Equal
&cntrl
imin = 0, irest = 0,
ntc=1, ntf=1,
ntpr=500, ntwx=500,
ntb = 0, cut = 14.0,
nstlim = 40000, nscm=0,
dt = 0.0005, ig=-1,
ntt = 3, gamma_ln=1000.0,
tempi=0.0, temp0=300.0,
tgtfitmask=":65,201,203,220",
tgtrmsmask=":65,201,203,220",
ineb = 1,skmin = 10,skmax = 10,
nmropt=1,
jfastw = 4,
fcap = 0.1,
/
&wt type='TEMP0', istep1=0,istep2=35000,
value1=0.0, value2=300.0
/
&wt type='END'
/
I'm using ntb=0 because I need to eventually use Amber/TeraChem to do QM/MM on the system, and I can't use periodic boundary conditions. I
probably do not need to use jfastw=4 though, but I was using this because there are some crystallization waters that interact with the protein,
and I didn't want to use TIP3P water. But, these interactions are not very important for NEB. Do you think I should run this simulation
with cut = 9999.9 and fast water, or is it a bad idea to run NEB with explicit water? Minimization with cut < 9999.9 seems to be problematic
for getting well minimized structures.
Thanks,
Jim
----- Original Message -----
From: "Daniel Roe" <daniel.r.roe.gmail.com>
To: "AMBER Mailing List" <amber.ambermd.org>
Sent: Wednesday, November 20, 2013 12:57:44 PM
Subject: Re: [AMBER] Nudged Elastic Band with Explicit Solvent for a Larger Protein
Hi,
Something is strange here. You say you're using explicit solvent but
you have ntb=0 in your minimization (i.e. no periodic boundaries) and
you have ntb=0 and igb=1 in your MD run (GB HCT implicit solvent
model). Trying to minimize or run MD on an explicit solvent system
with an implicit solvent model active will certainly lead to odd
results. If you haven't already I highly recommend you look at each
flag you are setting in your input and make sure you understand what
each one is doing. For example, you are setting jfastw=4, which turns
off fast SHAKE routines for waters; is there an explicit reason you
want to do this?
-Dan
On Wed, Nov 20, 2013 at 1:40 PM, James W. Snyder, Jr.
<jsnyder3.stanford.edu> wrote:
> Hey,
>
> I'm trying to run NEB for a protein with about 230 amino acids with an explicit solvent model. After minimizing the structures, I tried running NEB only to notice that the replicas tended to decrease in energy relative to the endpoints. I then went back and looked at my minimization files and noticed that the energy of the system didn't seem to decrease during minimization. If anything, it increased. When I set cut=9999.9, minimization seems to work fine, but I can't run NEB with a cut this large because it will take too long. This is the input file used for minimization,
>
> COMT-WT-NS-solvn : free 500 sd/1000 tot minimization
> &cntrl
> imin=1 ,
> ncyc=200 ,
> maxcyc=1000 ,
> ntb=0 ,
> ntwx = 5,
> cut=14.0 ,
> irest=0 , ntx=1 ,
> ntr=0 ,
> jfastw = 4,
> /
> END
>
> The file I used for NEB is,
>
> Alanine NEB initial MD with small K
> &cntrl
> imin = 0, irest = 0,
> ntc=1, ntf=1,
> ntpr=500, ntwx=500,
> ntb = 0, cut = 16.0, rgbmax=25.0,
> igb = 1, saltcon=0.2,
> nstlim = 40000, nscm=0,
> dt = 0.0005, ig=-1,
> ntt = 3, gamma_ln=1000.0,
> tempi=0.0, temp0=300.0,
> tgtfitmask=":65,201,203,220",
> tgtrmsmask=":65,201,203,220",
> ineb = 1,skmin = 10,skmax = 10,
> nmropt=1,
> jfastw = 4,
> fcap = 0.1,
> /
> &wt type='TEMP0', istep1=0,istep2=35000,
> value1=0.0, value2=300.0
> /
> &wt type='END'
> /
>
> Upon looking at this, I may not have been consistent with my use of cut, but I'm still concerned about the minimization step given that it seems to be increasing. Is it possible to run NEB with with explicit solvent and a cut < 9999.9? If so, how do I get a reasonable minimized structure to seed the NEB calculation with explicit solvent? I'm looking only for a local minima.
>
> Thanks,
>
> Jim Snyder
>
> _______________________________________________
> 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)
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Received on Wed Nov 20 2013 - 14:00:02 PST
