Re: [AMBER] problems in using autoimage

From: David A Case via AMBER <>
Date: Fri, 23 Sep 2022 12:26:45 -0400

On Thu, Sep 22, 2022, Giulia Sormani via AMBER wrote:

>Actually, I begin to think there is a problem with the density of the
>system, indeed if I run in the NPT, the volume doesn't oscillate, but it
>increases linearly and the simulation crashes.
>However, I don't understand what I am doing wrong in creating the
>topology. What I would like to do is to simulate a Zr4+ ion in a box of
>spc water (with 4 Cl- to neutralize). I would like to use 12-6-4 parameter
>I use the following tleap input:
>source leaprc.water.spce

Try just using this as a first step: it has parameters for Zr4+ that
presumably should work with spce water. See if you can get a stable
result with standard parameters before going on to use 12-6-4 parameters.
In any event, I would suggest first equilibrating without c4 parameters, and
then use that as a starting point for a subsequent simulation with c4

>loadamberparams frcmod.ions234lm_1264_spce #Load the 12-6-4 parameter set
>for +2, +3, and +4 metal ions for SPC/E water model
>i = createAtom ZR Zr4+ 4.0 #Create an atom i with atom name ZR, atom type
>Zr4+ and charge 4.0
>set i element "Zr" #Set element of atom i as Zr
>set i position { 0 0 0 } #Set coordinates of atom i as {0, 0, 0}
>r = createResidue ZR #Create a residue r with residue name ZR
>add r i #Add the atom i into residue r
>ZR = createUnit ZR #Create a unit ZR with unit name ZR
>add ZR r #Add the residue r into unit ZR

Since you created a new ZR unit, it's not clear to me where you got all of
the van der Waals parameters for this unit. Pengfei or others can chime in
here, but you should not need to create a new ion unit, as I understand
it. Please note that the zirconium ion in the atomic_ions is unit "Zr", but
you are defining and using a new unit called "ZR" (unit names are
case-sensitive). This is why it is important to check carefully what ion
parameters you have.

Bottom line: I think you can skip all the commands in the block above, and
work by modifying the prmtop file you would get by using just the "source
leaprc.water.spce" command.

....hope this helps....dac

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Received on Fri Sep 23 2022 - 09:30:02 PDT
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