Hi Tom,
Thanks for your inputs. I will delete the two previous parameter files to prevent confusion. So they will not be available in the coming AMBER releasing. And I will add new parameter files to AMBER based on the publications we published recently: https://pubs.acs.org/doi/abs/10.1021/acs.jcim.0c01390 <https://pubs.acs.org/doi/abs/10.1021/acs.jcim.0c01390> (about the -1 and +1 ions), https://pubs.acs.org/doi/abs/10.1021/acs.jctc.0c00194 <https://pubs.acs.org/doi/abs/10.1021/acs.jctc.0c00194> (about the +2 ions).
The intention to develop new parameters using pmemd.cuda is mainly because of the consideration of computational speed. In the current project, we developed parameters for -1, +1, +2, +3, and +4 metal ions for four new water models (OPC3, OPC, TIP3P-FB, and TIP4P-FB) in a systematic manner, which is a huge amount of work (the third paper, which is about the +3 and +4 ions, will be available in two months, if all things going well). In comparison, the previous parameters designed for Alexey were only for Na+, Cl- and K+ in conjugation with one water model (OPC). The good thing is that TI has been available in pmemd.cuda, so we decided to take advantage of that instead of using TI in sander, which is much slower than TI in pmemd.cuda. I hope it clarifies the issue.
-Pengfei
> On Feb 13, 2021, at 10:33 PM, Thomas Cheatham <tec3.utah.edu> wrote:
>
>
> I would suggest that this needs to be very clearly documented in the AMBER manuals to prevent confusion. Either the small differences do not matter or they are significant. If the small differences do not matter, why do we need new models? We need them only if differences are significant (and better). Yes, we have new papers with new parameters, but why should we use these unless significant improvement is seen, otherwise people are confused (sorry for reiterating). I will also reiterate, just because it is new, doesn't mean it is always better... Test, validate, assess and as dac would say, do not be afraid to experiment...
>
> --tec3
>
> ________________________________________
> From: Pengfei Li <ambermailpengfei.gmail.com>
> Sent: Saturday, February 13, 2021 4:58:03 PM
> To: AMBER Mailing List
> Subject: Re: [AMBER] OPC monovalent ion parameters
>
> Hi Chapin,
>
> The parameters already included in Amber (frcmod.ions1lm_126_hfe_opc and frcmod.ions1lm_126_iod_opc) were developed based on the personal request from Alexey, who wanted to get ion parameters for the OPC water model at that time. It used the protocol shown in the 2015 JCTC paper (https://pubs.acs.org/doi/10.1021/ct500918t), which used sander to do the thermodynamic integration (TI) calculations.
>
> There are small differences between the parameters in the frcmod files already included in Amber (frcmod.ions1lm_126_hfe_opc and frcmod.ions1lm_126_iod_opc) and the parameters in the paper just published (https://doi.org/10.1021/acs.jcim.0c01390). The reason is because the previous parameters were obtained based on TI in sander, while the parameters in the recent paper just published were obtained based on the TI implemented in pmemd.cuda. The TI implementations in sander and pmemd.cuda are not exactly the same, but they should give similar results. For consistency of the citation purpose, I suggest one to use the new parameters which were just published if they have not carried out any production simulations.
>
> Hope it helps,
> Pengfei
>
>> On Feb 13, 2021, at 1:50 PM, Cavender, Chapin <Chapin_Cavender.URMC.Rochester.edu> wrote:
>>
>> Dear Amber community,
>>
>> Ken Merz has recently (Feb 4, 2021) published monovalent ion parameters specific for the OPC3, OPC, TIP3P-FB, and TIP4P-FB water models: https://doi.org/10.1021/acs.jcim.0c01390
>>
>> However, it appears that these parameters differ from the frcmod files included in Amber, frcmod.ions1lm_126_hfe_opc and frcmod.ions1lm_126_iod_opc. Presumably, these parameters were derived in the same way as the parameters for other water models described in https://doi.org/10.1021/ct500918t, but neither the manual nor the frcmod files provide a reference. However, it seems like the methodology to derive the parameters is similar between these two publications, so I don't understand why the frcmod parameters are different from the recently published ones.
>>
>> Does anyone in the community know the source for the parameters in the Amber frcmod files? In particular, is the 2015 JCTC paper from Li, Song, & Merz the correct reference for these frcmod files?
>>
>> Best,
>> Chapin Cavender
>> PhD student, Dave Mathews lab
>> Department of Biochemistry & Biophysics
>> University of Rochester School of Medicine & Dentistry
>> ----------------------------------------------------------------------
>>
>> Message: 1
>> Date: Mon, 25 Jan 2021 15:35:11 -0500
>> From: Carlos Simmerling <carlos.simmerling.gmail.com>
>> Subject: Re: [AMBER] OPC monovalent ion parameters
>> To: AMBER Mailing List <amber.ambermd.org>
>> Message-ID:
>> <CAGk3s-SOJn2qtuAmr7D_QhpR6kSfiNcbA31wVxF9XJ3GhFKqPw.mail.gmail.com>
>> Content-Type: text/plain; charset="UTF-8"
>>
>> I'd check this:
>> Developing Monovalent Ion Parameters for the Optimal Point Charge (OPC)
>> Water Model
>> Daniel E Clark John C Dood Brent P Krueger
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__doi.org_10.1096_fasebj.31.1-5Fsupplement.761.24&d=DwICAg&c=4sF48jRmVAe_CH-k9mXYXEGfSnM3bY53YSKuLUQRxhA&r=E2G_FiEtGhStTPYmNtsKk1lRtqjn8haGVq3W8F23rEPZ9zK1SwNK3Gk-rV9NMQ5E&m=tEy6OOqSZ9EMJPKqXZkDwCJFyjHeHwlzTz1O1Njnmuw&s=FaaSRVDO8kO3GYMmdMBF9F65ne0UFzGUdTeKAxbkjFs&e=
>>
>> On Mon, Jan 25, 2021 at 1:07 PM Sebastian Oleksy <so389.chem.rutgers.edu>
>> wrote:
>>
>>> Hello,
>>>
>>> I will be running MD simulations on a nucleic acid system, using the
>>> 4-site OPC water model in combination with the RNA.OL3 force field. I was
>>> wondering what specific monovalent ion parameters would be best to use here
>>> ? Li/Merz 12-6 HFE set, 12-6 IOD set, or even J/C_tip4pew? Others? Or would
>>> perhaps OPC3 be better than the 4-site OPC model for this? If anyone has
>>> any experience or guidance, it would be much appreciated. Thank you.
>>>
>>> Respectfully,
>>> Sebastian Oleksy
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.ambermd.org_mailman_listinfo_amber&d=DwICAg&c=4sF48jRmVAe_CH-k9mXYXEGfSnM3bY53YSKuLUQRxhA&r=E2G_FiEtGhStTPYmNtsKk1lRtqjn8haGVq3W8F23rEPZ9zK1SwNK3Gk-rV9NMQ5E&m=tEy6OOqSZ9EMJPKqXZkDwCJFyjHeHwlzTz1O1Njnmuw&s=EwOpyWb05Tc7VmUuZzxOfntrC5AUM_-M4INAecTXnto&e=
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Feb 15 2021 - 09:00:02 PST
