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water ion parameter
#37608 08/15/19 06:44 PM
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aad Offline OP
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Hello,
I am trying to reproduce some of the diffusion characteristics and free energy of solvation of OH- ion in water using charmm. However with the current topology and parameter as specified in the toppar_water_ions.str file I am unable to do so. Specifically i am interested in changing the LJ potential of OH-. Below is how this parameter is specified currently:-

!TIP3P LJ parameters
HT 0.0 -0.046 0.2245
OT 0.0 -0.1521 1.7682

!for hydroxide
OX 0.000000 -0.1521 1.7682 ! ALLOW POL ION
! JG 8/27/89
HX 0.000000 -0.044000 0.2245 ! ALLOW PEP POL SUL ARO ALC
! same as TIP3P hydrogen, adm jr., 7/20/89

Is there any way to find out what these numbers exactly mean? or why is the first column zero and the second negative? the second and third column seem to correspond with the epsilon and sigma values respectively but the negative value is still confusing.

Last edited by aad; 08/15/19 07:42 PM.
Re: water ion parameter
aad #37609 08/15/19 08:07 PM
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L-J parameters can be specified in two ways in CHARMM, but today only one is used. The 0.0 in the first column is not used. Column two is the well-depth and column 3 is 0.5 * Rmin, where Rmin is the distance between two atoms of the same type at which the L-J energy is at its minimum.

See parmfile.doc (or parmfile.info)

I am not so sure about the quality of the hydroxide parameters - these ions are pretty rare (pronunciation 'non-existent') in classical simulations. At pH 7 you would need a fairly large box to have one OH- ... (


Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden
Re: water ion parameter
aad #37611 08/15/19 09:20 PM
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aad Offline OP
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Thank you Dr. Nilsson that makes a lot of sense.
On reviewing recent papers it looks like some manipulation of the OH- parameter is required to reproduce experimental outcome.

Making any changes to these parameter however, give an extensive shake error message in the output file although the code does run through with normal termination and a warning at level -2, but I think with the information you provided here I can work around that issue as well.

Best,
aad

Re: water ion parameter
aad #37612 08/15/19 09:28 PM
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-2 warnings should not be ignored, unless you know very, very well what you are doing - do you?. I don't really see why changes to the L-J parameters should give SHAKE errors.


Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden
Re: water ion parameter
aad #37614 08/15/19 11:30 PM
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rmv Offline
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Bad model building can lead to numerous SHAKE errors, so perhaps some small scale tests might be a good starting point. The -2 error should be fixed before proceeding, and a small scale test could make that easier. If the OH- molecule will be a key part of your project, rigorous testing if any parameter changes is highly recommended.


Rick Venable
computational chemist

Re: water ion parameter
aad #37615 08/16/19 12:17 AM
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aad Offline OP
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Thank you for your inputs.
I have read in many prior threads that error in SHAKE is generally a symptom rather than a true cause. I have actually run this simulation (it is small scale with 923 TIP3P molecules and 1 OH- molecule in PBC) with no errors when the LJ parameters are not changed at all. However even with slight change in the LJ parameter I tend to find this error message in my output file. So it does seem like a changing LJ parameters is where the error is coming from.
I can upload the relevant files tomorrow but I am guessing since this specifies the non bonded interactions, changing the cutoff specs will fix this error?

Re: water ion parameter
aad #37616 08/16/19 02:11 AM
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The standard cutoffs from the parameter file should be used; fix the error.

By small, I meant a few molecules. I'd start with just an OH- ion; evaluate the energy for both sets of L-J values, maybe a short minimization with SHAKE. Then try the same with a few waters, or maybe just OH- and one water and move them closer and closer via COOR TRANslate.


Rick Venable
computational chemist

Re: water ion parameter
aad #37617 08/16/19 06:45 PM
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aad Offline OP
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Dr. Venable,
I just tried evaluating the energies of just an OH- ion with different parameters. It's an excellent idea however it seems like toppar_water_ions.str does not specify any bonded energy parameter for OH- and treats it as a stand alone ion. After the simulation with a short minimization and shake (it runs well with most severe warning at level O) my out put file gives me zero for energy value for both my parameters of interest. I will be trying out your second suggestion with the usage of COOR TRAN command shorty and update this thread.


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