[AMBER] The protein is Leaving the water box!

From: Amber mail <amber.auc14.gmail.com>
Date: Fri, 14 Aug 2015 02:36:59 +0200

Dear AMBER users,

I am performing a MD simulation using AMBER12 under the ff99SB force filed.
Initially, the structure was neutralized and then solvated using TIP3P
water model.

After the minimization stage, a 50ps of MD simulation was performed from 0K
to 100K. The system is then heated up in increments of 25K with 50ps of MD
simulation at each temperature increment until the desired temperature of
310K was established.

This the control file for heating (0-100)K

Heat
> &cntrl
> imin=0,
> ntx=1,
> irest=0,
> nstlim=25000,
> dt=0.002,
> ntf=2,
> ntc=2,
> tempi=0.0,
> temp0=100.0,
> ntpr=100,
> ntwx=100,
> cut=8.0,
> ntb=2,
> ntp=1,
> ntt=3,
> gamma_ln=1.0,
> tautp=1.0,
> taup=1.0,
> pres0=1.01325,
> nmropt=0,
> ig=-1,
> iwrap=1,
> /
>

A 50 ns of MD simulation is going to be performed at 310K. Till now, I have
got 20 ns out of 50 ns. This is the control file for the production step

Production
> &cntrl
> imin=0,
> ntx=5,
> irest=1,
> nstlim=5000000,
> dt=0.002,
> ntf=2,
> ntc=2,
> temp0=310.0,
> tempi=310.0,
> ntpr=5000,
> ntwx=5000,
> cut=8.0,
> ntb=2,
> ntp=1,
> ntt=3,
> gamma_ln=1.0,
> ig=-1,

  nmropt=0,
> iwrap=1,
> /
>

The problem is that a part of the protein is leaving the water box after 20
ns of the MD production



Please correct me If I am wrong, since I used the wrapping option
(iwrap=1), the water molecules should wrap (surround) any residue in case
if it is trying to leave the water box. does this mean that these outer
residues are being simulated now in vacuum?! If I am right, is setting
ntb=2 (boundary conditions) works for this behavior, and there is no
problem ?!


Another question regarding the heating stage, below is the plot of
Temperature vs. Time before production, I am wondering why the increase in
the Temperature was not going smoothly and the equilibration did not reach
at the end of the heating stage (like the results of the tutorials, which I
performed before)


​A same pattern (sudden change) was also obtained for the Potential energy,
Kinetic Energy and the Total Energy (in the heating stage)

Thanks in advance!





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262L-leaving_the_WB.png
(image/png attachment: 262L-leaving_the_WB.png)

heating.png
(image/png attachment: heating.png)

Received on Thu Aug 13 2015 - 18:00:04 PDT
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