Hi all,
I am currently puzzled by the emphasis on using an acceptance ratio of
around 0.2 for replica exchange simulations in the literature.
This optimum ratio is, as far as I understand, derived assuming that
the exchange attempt frequency is constant and that the protein
dynamics are not limit
On Mon, Jan 9, 2012 at 3:46 PM, Mark Abraham wrote:
> On 10/01/2012 7:19 AM, Ben Reynwar wrote:
>
> On Tue, Dec 20, 2011 at 7:16 PM, Mark Abraham
> wrote:
>
> On 12/19/2011 1:51 PM, Ben Reynwar wrote:
>
> I'm having a problem with gromacs not terminating as expected
On Tue, Dec 20, 2011 at 7:16 PM, Mark Abraham wrote:
> On 12/19/2011 1:51 PM, Ben Reynwar wrote:
>>
>> I'm having a problem with gromacs not terminating as expected when
>> using the maxh option.
>> It is an REMD simulation with 32 replicas.
>> I'm
I'm having a problem with gromacs not terminating as expected when
using the maxh option.
It is an REMD simulation with 32 replicas.
I'm specifying -maxh 24 and as expected see the following in the stderr output.
Step 773882: Run time exceeded 23.760 hours, will terminate the run
Step 773876: Run
The exchange probability will just effect the computational
efficiency. It's entirely possible that it won't even effect that,
since the dynamics of the replica flow up and down the temperature
range may be limited by the dynamics of your protein rather than the
exchange frequency and probabilitie
On Fri, Nov 18, 2011 at 8:07 PM, Mark Abraham wrote:
> On 19/11/2011 6:42 AM, Ben Reynwar wrote:
>>
>> On Fri, Nov 18, 2011 at 7:23 AM, Mark Abraham
>> wrote:
>>>
>>> On 18/11/2011 8:10 AM, Ben Reynwar wrote:
>>>>
>>>> Dear gromacs
On Fri, Nov 18, 2011 at 7:23 AM, Mark Abraham wrote:
> On 18/11/2011 8:10 AM, Ben Reynwar wrote:
>>
>> Dear gromacs list,
>>
>> Does anyone know how well current force fields capture the energetics
>> of non-specific protein-protein interactions? I'm si
Dear gromacs list,
Does anyone know how well current force fields capture the energetics
of non-specific protein-protein interactions? I'm simulating a
protein with an arm that alternates between (apparently) non-specific
adsorption to the main-body of the protein and free movement in the
solvent
On Thu, Oct 27, 2011 at 4:09 PM, Mark Abraham wrote:
> On 28/10/2011 9:29 AM, Ben Reynwar wrote:
>>
>> I found a post on the devel list from a couple of weeks ago where a
>> fix is given and it appears to work for me.
>> The link is
>> http://lists.gromacs.
e testing (e.g. Do different parallel regimes produce the same
> symptoms? Can the individual replicas run in a non-REMD simulation?) and
> file a Redmine issue with your observations and a small sample case.
>
> Mark
>
>>
>> Cheers,
>> --
>> Szilárd
>>
>&g
Hi all,
I'm getting errors in MPI_Allreduce what I restart an REMD simulation.
It has occurred every time I have attempted an REMD restart.
I'm posting here to check there's not something obviously wrong with
the way I'm doing the restart which is causing it.
I restart an REMD run using:
--
I posted to the list a few days ago with an energy drift problem.
Mark Abraham helpfully suggested using all-bonds rather than h-bonds
which solved the problem. I'm now trying to understand quite why that
helped so much.
The simulation is a protein of about 5000 atoms using GBSA, a time
step of 2
On Fri, Oct 14, 2011 at 9:11 AM, Mark Abraham wrote:
> On 14/10/2011 10:12 AM, Ben Reynwar wrote:
>>
>> Hi gromacs list,
>>
>> I'm about to start some REMD simulations using generalized Born
>> solvent on a protein of about 5000 atoms. I have two questions,
Hi gromacs list,
I'm about to start some REMD simulations using generalized Born
solvent on a protein of about 5000 atoms. I have two questions, the
first of which is about gromacs, the second more about REMD in
general.
(1)
I'm getting some pretty ugly energy drift (300K->500K in 1 ns) for an
N
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