Hi Ying-Chieh,
The plan was to have TI support on GPUs finalized (and made into an end
user product rather than the experimental stuff I have talked about at
conferences) for the AMBER 14 release but a number of different events
transpired that meant we didn't have time to finish it for the release. We
are still working on it and the plan is to release a free update that will
automatically add it through AMBER 14's autoupdate mechanism in a few
months. For now it is just the CPU version of pmemd that supports TI.
All the best
Ross
On 5/14/14, 8:42 PM, "Ying-Chieh Sun" <sun.ntnu.edu.tw> wrote:
>Hi Ross,
>
>Thanks so much for the suggestions. They are very helpful. ... in
>addition,
>I would like to ask another question about if pmemd.cuda and/or
>pmemd.cuda.MPI support TI computations?
>
>It looks to me ... yes they should according to your webpage info: poster
>2013" Ross C. Walker - "Fast and Reliable Ligand Binding Free Energies -
>Thermodynamic Integration on GPUs", Gordon Research Conference on Computer
>Aided Drug Design, Mount Snow Resort, Vermont, USA, Jul 2013."
>
>However, on amber pages or amber14 manual, the information is not clear to
>me. ... the information are mostly about regular MD instead of free energy
>calculation.
>
>Sorry that, I could have been compiling myself and tested but the software
>installation support here is not so handy, and we are in a process
>evaluating buying (and use up budget in time) GPU machine(s) now. So I ask
>for help here.
>
>Thanks very much again.
>
>Ying-chieh
>
>-----Original Message-----
>From: Ross Walker [mailto:ross.rosswalker.co.uk]
>Sent: Wednesday, May 14, 2014 11:06 PM
>To: AMBER Mailing List
>Subject: Re: [AMBER] thermodynamic integration (TI) simulation: pmemd of
>amber14 vs sander of amber11- vdw transformation
>
>Hi Ying-Chieh,
>
>To add some more to what Jason said - accepting the fact that your
>simulation parameters appear to be very different (are you definitely
>using
>softcore in amber11 for example) this also looks to me like a case of the
>results being hopelessly under converged. 600,000 steps is only 1.2ns
>which
>likely means your error bars on the sampling are huge. So a good chunk of
>that difference could be coming from there. Try doing 5 or so repeats of
>your AMBER 11 calculations with different random seeds / initial
>structures
>and see what the variation is in the results you get.
>As with any paper I receive where people do free energy calculations I
>always ask them to do multiple repeats or ideally plot the free energy
>obtained as a function of cumulative sampling length - the last one people
>rarely do - I think because when they try it it is a real eye opener into
>how unconverged the calculations typically are. You try this yourself to
>see.
>
>Take you 600K steps from the AMBER 11 simulation. Throw away all but the
>first 10K and calculate the delta delta G and then plot that on a graph
>where the X axis is sample points and the Y axis the DDG obtained. Then
>repeat throwing away all but the first 20K, add that to the plot. Then
>30K,
>then 40K etc all the way up to the full 600K - it's probably best to
>script
>this. See what the plot looks like and it should give you a nice visual
>idea
>of how the run is converging.
>
>All the best
>Ross
>
>
>On 5/14/14, 4:37 AM, "Jason Swails" <jason.swails.gmail.com> wrote:
>
>>On Wed, 2014-05-14 at 18:21 +0800, Ying-Chieh Sun wrote:
>>> Hi,
>>>
>>>
>>>
>>> We are learning TI computation for protein-ligand binding using pmemd
>>>of amber14. We used 3-step protocol ((1)switch charge off, (2) vdw
>>>transformation, (3)switch charge back on) to compute Delta Delta G of
>>>two ligand binding with the same protein.
>>>
>>>
>>>
>>> The results of the vdw transformation are summarized below:
>>>
>>>
>>>
>>> Delta G (Complex) Delta G(Solution)
>>>
>>> -1.6746+-4.7307 -0.4455+-4.0797 (pmemd of amber14: ligand charge:
>>>BCC
>>> charge!)
>>>
>>> -10.8895+-6.0608 -13.1352+-5.4417 (sander of amber11: ligand charge:
>>>RESP
>>> charge!)
>>>
>>>
>>>
>>> Because we used BCC charge this time for pmemd, we have not used RESP
>>>charge yet. But, in the vdw transformation, the charges are off.
>>>Therefore, I think the Delta G (not Delta Delta G) should be similar.
>>>But they differ by
>>>~10
>>> kcal/mol in the complex and solution computations, respectively. The
>>>Delta Delta G©ös are indeed in the similar range.
>>
>>The TI code in pmemd is quite new and using it is radically different
>>than using the TI code in sander. Therefore, I would suggest changing
>>as _few_ things as possible when carrying out your comparisons. (i.e.,
>>make sure you are using exactly the same parameters in both cases to
>>carry out your simulations for comparison). Any attempt to explain the
>>discrepancy will most likely be unsubstantiated speculation.
>>
>>>
>>>
>>>
>>> Any advice/suggestions are appreciated.
>>>
>>>
>>>
>>> We also found a typo, I think, in the output file. As shown below, it
>>>should
>>> be ©øA V E R A G E S O V E R 600000 S T E P S©÷ instead of 3000 S T
>>>E P
>>> S.
>>
>>No, this is correct. pmemd does not compute the energy every step (it
>>only computes the energy on the steps that it needs to print the
>>energy). This is done because computing the energy introduces an
>>unnecessary computational cost (and if you don't need the energy, why
>>compute it?). So my guess is that you printed every 200 steps for
>>600,000 total steps...
>>
>>HTH,
>>Jason
>>
>>--
>>Jason M. Swails
>>BioMaPS,
>>Rutgers University
>>Postdoctoral Researcher
>>
>>
>>_______________________________________________
>>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 Wed May 14 2014 - 21:30:03 PDT
