Re: [AMBER] problems in using autoimage

From: Giulia Sormani via AMBER <>
Date: Wed, 28 Sep 2022 14:08:51 +0200

Hello Dave,

actually things are working nicely if I do all the steps to equilibrate
the system using the standard 12-6 LJ, and then take the last
configuration to run the NVT simulation with 12-6-4 LJ.
I didn't encounter this problem when I was simulating an organic molecule
with a Zr ion.
Still, now the problem seems to be solved.

Many thanks!


> 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
> parameters.
>>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 Wed Sep 28 2022 - 05:30:03 PDT
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