The system goes out of equilibrium, because in the current hremd implementation, right after successful exchange the system has new coordinates (from its neighbor) and old velocities. In other words, the velocities and coordinates don't match right after successful exchange and the system goes out of equilibrium. This problem is bolder when you use the shake (we have tested that). The easiest solution is to exchange both coordinates and velocities at the exchange time.
This problem doesn't happen to TREMD because in its implementation, temperatures exchange not the coordinates.
Best,
Danial Sabri Dashti
Quantum Theory Project &
Physics Department
University of Florida
Ph.D. Graduate Student
________________________________
From: Carlos Simmerling <carlos.simmerling.gmail.com>
To: AMBER Mailing List <amber.ambermd.org>; dani sd <daniandphy.yahoo.com>
Sent: Wednesday, August 15, 2012 3:58 PM
Subject: Re: [AMBER] Temperature regulation in HREMD
If the exchange is successful, how can the system be out of equilibrium? In correct remd, acceptance of exchange implies that the structures are valid members of both ensembles.
On Aug 15, 2012 2:40 PM, "dani sd" <daniandphy.yahoo.com> wrote:
Hi Brian,
>
>I think the problem is coming from HREMD code. After each successful exchange, there is a relaxation time, which is related to the natural fluctuation of the system. In the current implementation, the system will be out of equilibrium for a while after each successful exchange. This problem is bold especially in the big systems because of large relaxation times.
>We solved the problem by modifying the code, however the modification is not uploaded to the amber repository. I will send the modified HREMD code to your email and you can recompile "sander.MPI".
>Hope it solves the problem.
>
>Best,
>Danial
>
>
>Danial Sabri Dashti
>Quantum Theory Project &
>Physics Department
>University of Florida
>Ph.D. Graduate Student
>
>
>________________________________
>
>
>From: Brian Radak <radak004.umn.edu>
>Date: Wed, Aug 15, 2012 at 9:39 AM
>Subject: [AMBER] Temperature regulation in HREMD
>To: AMBER Mailing List <amber.ambermd.org>
>
>
>I am running HREMD and have observed what seems to be unexpected behavior
>in the instantaneous temperature. That is, although all of the replicas are
>propagated using Langevin dynamics at 300K, the average temperatures are
>generally around 270-280K. There is also a large variance in the total
>energy (about 1000 kcal/mol), although perhaps this is ok and I am just not
>understanding the output (do the mdout files track the replicas or track
>the coordinates?)
>
>I am using a patched version of AMBER 12. The system is a histidine residue
>in a ~50 A box of TIP4P-Ew water. There are 12 replicas (although I also
>observed this with 2 replicas) which consist of the atomic charges being
>linearly scaled between the protonated and deprotonated forms (this was
>accomplished using parmed). No changes to the atom types were performed.
>
>All replicas had the same mdin:
> &cntrl
> nstlim = 250, numexchg = 1000, dt = 0.002,
> ntpr = 250, ntwx = 250,
> ntwr = 250000,
> ioutfm = 1, iwrap = 1, ig = -1,
> ntc = 2, ntf = 2,
> cut = 9,
> ntt = 3, temp0 = 300.0, tempi = 300.0, gamma_ln = 1.0
> /
> &ewald
> dsum_tol=1.0e-6
> /
>
>The starting structures were generated by 200 ps of constant pressure
>Langevin dynamics with no exchanges and then all of the box coordinates
>changed to be the same. I thought it might have been a mistake not to use
>irest = 1 when starting REMD, but am reluctant to blame that for the
>observed behavior.
>
>The free energies seem to be well converged based on the last 2 entries
>from the remlog, but I'm sure this could just be misleading:
>
># Rep#, Neibr#, Temp0, PotE(x_1), PotE(x_2), left_fe, right_fe, Success,
>Success rate (i,i+1)
># exchange 999
> 1 12 300.00 -44753.10 -44571.23 -2.76 0.00 F
>0.66
> 2 3 300.00 -44301.78 -44699.62 0.00 -2.87 T
>0.37
> 3 2 300.00 -44696.59 -44298.66 2.82 0.00 T
>0.40
> 4 5 300.00 -44632.76 -44140.71 0.00 -0.41 F
>0.40
> 5 4 300.00 -44142.14 -44631.30 0.54 0.00 F
>0.43
> 6 7 300.00 -44282.42 -44425.70 0.00 1.75 F
>0.52
> 7 6 300.00 -44427.33 -44282.56 -1.74 0.00 F
>0.45
> 8 9 300.00 -44584.41 -44984.53 0.00 3.62 F
>0.52
> 9 8 300.00 -44988.08 -44586.89 -3.60 0.00 F
>0.50
> 10 11 300.00 -44692.44 -44763.92 0.00 5.55 T
>0.53
> 11 10 300.00 -44769.07 -44697.58 -5.52 0.00 T
>0.71
> 12 1 300.00 -44618.67 -44713.88 0.00 -33.86 F
>0.00
># exchange 1000
> 1 2 300.00 -44275.48 -44811.39 0.00 -1.91 T
>0.66
> 2 1 300.00 -44809.19 -44273.45 1.89 0.00 T
>0.37
> 3 4 300.00 -44737.41 -44249.38 0.00 -1.63 F
>0.40
> 4 3 300.00 -44248.15 -44735.31 1.57 0.00 F
>0.40
> 5 6 300.00 -43832.07 -43837.66 0.00 0.62 T
>0.44
> 6 5 300.00 -43838.34 -43833.08 -0.71 0.00 T
>0.52
> 7 8 300.00 -43958.10 -44146.05 0.00 2.64 T
>0.46
> 8 7 300.00 -44148.87 -43960.69 -2.73 0.00 T
>0.52
> 9 10 300.00 -44596.36 -44997.54 0.00 4.56 F
>0.50
> 10 9 300.00 -45002.94 -44600.83 -4.63 0.00 F
>0.53
> 11 12 300.00 -44792.55 -44199.67 0.00 3.14 F
>0.71
> 12 11 300.00 -44202.75 -44795.50 -3.16 0.00 F
>0.00
>
>
>Am I doing something ill advised here or making some other silly error?
>
>Thanks,
>Brian
>
>--
>================================ Current Address =======================
> Brian Radak : BioMaPS
>Institute for Quantitative Biology
> PhD candidate - York Research Group : Rutgers, The State
>University of New Jersey
> University of Minnesota - Twin Cities : Center for Integrative
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>radakb.biomaps.rutgers.edu
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>address.
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>
>--
>Jason M. Swails
>Quantum Theory Project,
>University of Florida
>Ph.D. Candidate
>352-392-4032
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Received on Wed Aug 15 2012 - 14:00:04 PDT
