[gmx-users] Temperature interval in REMD simulations

[Kalyanashis Jana]

Dear gromacs user,
I am trying to do REMD simulation for protein having 8320 atoms (including
protons). The total protein-drug system is solvated with 34269 TIP4P water
molecules. I have checked for the temperatures (298.00 to 340.00 K) and no
of replicas at "http://folding.bmc.uu.se/remd/" with an exchange
probability 0.3. It has suggested 56 replicas and temperatures with
r=1.0023, the common ratio of the geometric progression. However, it will
be computationally too costly to perform REMD of such a big system with 56
replicas.


Could you please suggest me, what temperature limit and exchange
probability is enough to produce reasonable results?

Thanks in advance,
Kalyanashis Jana

On Thu, Nov 17, 2016 at 6:11 PM, Kalyanashis Jana <kalyan.chem.in at gmail.com>
wrote:

> Dear gromacs user,
> I am trying to do REMD simulation for protein having 8320 atoms (including
> protons). The total protein-drug system is solvated with 34269 TIP4P
> water molecules. I have checked for the temperatures (298.00 to 340.00 K)
> and no of replicas at "http://folding.bmc.uu.se/remd/" with an exchange
> probability 0.3. It has suggested 56 replicas and temperatures with
> r=1.0023, the common ratio of the geometric progression. However, it will
> be computationally too costly to perform REMD of such a big system with 56
> replicas.
>
>
> Could you please suggest me, what temperature limit and exchange
> probability is enough to produce reasonable results?
>
> Thanks with advance,
> Kalyanashis Jana
>
>
>
>
>
>
> On Fri, Aug 19, 2016 at 5:40 PM, Florent Hédin <work at fhedin.com> wrote:
>
>> Dear Ishrat, and dear other gmx-users
>>
>> I once used the following website, which can help you generating a
>> temperature set for REMD simulations
>>
>> http://folding.bmc.uu.se/remd/
>>
>> It is may be the tool you already used for generating you 18
>> temperatures, by the way. By trying different values for the 'exchange
>> probability' field you can change the number of temperatures.
>>
>> It depends on the system size and the number of water molecules of
>> course, but try with a larger exchange probability, 0.3 0.4 or 0.5
>> should increase your number of replica.
>>
>> Regards,
>>
>> Florent Hédin
>>
>> On 19/08/16 12:12, asaffarhi at post.tau.ac.il wrote:
>> > Dear Ishrat,
>> >
>> > Roughly speaking, the temperatures should be chosen so the acceptance
>> > rates between replicas in adjacent temperatures are kept relatively
>> > constant. The high temperature should be such that k_B*T_high should be
>> > similar to the energy barriers relative to the "equilibrium state". From
>> > T_high and up your results should not change.
>> >
>> > You can take a look at the last paragraph in the appendix of
>> > http://www.sciencedirect.com/science/article/pii/S0378437113006468
>> >
>> > In addition there is also Hamiltonian REMD (H-REMD) in which the
>> > temperature is kept constant and lambda is used instead (not having to
>> > worry about the speed of the atoms at high temperatures).
>> >
>> > See for example
>> > https://arxiv.org/pdf/1310.2112v17.pdf, Sec. VI
>> >
>> > There are references in both links.
>> >
>> > Best,
>> > Asaf
>> >
>> > Quoting ISHRAT JAHAN <jishrat17 at gmail.com>:
>> >
>> >> Dear all
>> >>
>> >> I am trying to perform REMD simulation of small peptide. I am doing
>> REMD
>> >> first time. I am not sure how to decide the temperature interval in a
>> >> given
>> >> range. I have used temperature generator for REMD-simulations for 290
>> >> K to
>> >>  500 K with exchange probability of 0.25. It gives 18 replicas.
>> However I
>> >> am repeating the work done by Zachary et al. I am giving the link here.
>> >> http://www.ncbi.nlm.nih.gov/pubmed/25691742
>> >>
>> >>
>> >> There are 62 replicas generated with temperature range of 290 to 500 K.
>> >>
>> >> Can anyone tell me how to generate 62 replica with temperature range
>> >> of 290
>> >> to 500 K and also tell how to decide the temperature interval for doing
>> >> REMD.
>> >> How temperature is related to the number of replicas.
>> >>
>> >>
>> >>
>> >> Thanks in Advance
>> >> --
>> >> Gromacs Users mailing list
>> >>
>> >> * Please search the archive at
>> >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> >> posting!
>> >>
>> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> >>
>> >> * For (un)subscribe requests visit
>> >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> >> send a mail to gmx-users-request at gromacs.org.
>> >
>> >
>> >
>>
>> --
>> Florent Hédin
>> work at fhedin.com <mailto:work at fhedin.com>
>> Public GPG KEY
>> <https://pgp.mit.edu/pks/lookup?op=get&search=0xBAAE5B1AB2E702B4>
>>
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at http://www.gromacs.org/Support
>> /Mailing_Lists/GMX-Users_List before posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-request at gromacs.org.
>>
>
>
>
> --
> Thanks with regards
> Kalyanashis Jana
>



-- 
Thanks with regards
Kalyanashis Jana