Re: [gmx-users] Energy drift combining tabulated potentials and group cut-off.

[serpercon]

Hello, 

My apollogies, the drift is present whether I use tabulated potentials
or not. The email's title I chose is misleading. If I am not mistaken I
am using a buffer when I put rcut= 1.0 and rlist=1.3 , but this was not
entirely clear to me using with the manual.  

Sergio 

El 05/09/2017 12:29, Mark Abraham escribió:

> Hi,
> 
> Your earlier email implied that the drift was present when you used the
> group cutoff-scheme, whether or not you used tabulated interactions. But
> just now you implied something different. Unbuffered cutoffs with the group
> scheme are not comparable with e.g. the default buffering used with the
> Verket scheme.
> 
> Mark
> 
> On Mon, Sep 4, 2017 at 10:56 AM  wrote:
> 
> Hello,
> 
> Thank you very much for your thoughtfull response. The structural
> properties seem to be represented correctly so I guess it should work. I
> know that drifts are something we must live with but since it appeared
> when changing the system to a tabulated potential+a group cutoff I was
> not sure if I was making some mistake.
> 
> Sergio
> 
> El 01/09/2017 12:48, Mark Abraham escribió:
> 
> Hi,
> 
> There's not easy answers to such questions. A practical implementation of
> MD that can actually do most relevant kinds of science in relevant time
> frames can't have bitwise conservation. Drift accumulates from multiple
> aspects of the implementation, too, including the system size, and
> constraint algorithm, which can dominate over the effects of missing
> interactions over the lifetime of pair lists. See the discussion in the
> GROMACS reference manual, e.g. figure 3.5.
> 
> One proper question to ask is at what point your protocol correctly models 
> whatever relevant physical data exists that is relevant to what you want to 
> observe. Drift that is too large is likely to affect observables, but will 
> affect different ones differently.
> 
> Mark
> 
> On Fri, Sep 1, 2017 at 12:12 PM  wrote:
> 
> Dear GROMACS Community,
> 
> I am trying to do a simulation using a tabulated potential which forces
> me to use the group cut-off. I get a drift in the conserved quantity of
> -600KJ/mol/ns. My system consists of 1000 rigid TIP4P water molecules
> and a Na+ ion. I imagine that eventhough it will soon be deprecated the
> group cutoff scheme still works correctly. I have tryed to change the
> parameters without success and in any case the ones I use seem
> reasonable (in my experience using other programs). The rdfs of the
> system look normal so I ruled out topology problems.
> 
> It seems that the problem is in the group cut-off since
> when I change the tabulated potential for a regular vdw the problem
> persists. I have followed the instructions of:
> 
> http://www.gromacs.org/@api/deki/files/94/=gromacs_nb.pdf
> 
> to implement the tabulated potentials.
> 
> Is this the kind of energy drift acceptable? I have pasted a copy .mdp
> 
> Thanks for your help,
> 
> Sergio Perez-Conesa
> 
> integrator = md
> dt = 0.001
> nsteps = 10
> init-step = 0
> cutoff-scheme = group
> nst-list = 1
> verlet-buffer-tolerance = 0.0005
> ns-type = grid
> rlist = 1.3
> pbc = xyz
> coulombtype = PME-switch
> rcoulomb = 1.
> rcoulomb-switch = 0.95
> pme-order = 4
> fourierspacing = 0.1
> ewald-rtol = 1.e-5
> vdwtype = user
> rvdw = 1.0
> DispCorr = No
> tcoupl = v-rescale
> tc-grps = System
> ;nsttcouple = 1
> tau-t = ref-t = 300.0
> constraints = all-angles
> constraint-algorithm = LINCS
> lincs_iter = 1
> lincs_order = 4
> energygrps = NA OW
> energygrp_table = NA OW
> comm-mode = linear
> --
> Gromacs Users mailing list
> 
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Re: [gmx-users] Energy drift combining tabulated potentials and group cut-off.

[serpercon]

Hello, 

Thank you very much for your thoughtfull response. The structural
properties seem to be represented correctly so I guess it should work. I
know that drifts are something we must live with but since it appeared
when changing the system to a tabulated potential+a group cutoff I was
not sure if I was making some mistake.  

Sergio 

El 01/09/2017 12:48, Mark Abraham escribió:

> Hi,
> 
> There's not easy answers to such questions. A practical implementation of
> MD that can actually do most relevant kinds of science in relevant time
> frames can't have bitwise conservation. Drift accumulates from multiple
> aspects of the implementation, too, including the system size, and
> constraint algorithm, which can dominate over the effects of missing
> interactions over the lifetime of pair lists. See the discussion in the
> GROMACS reference manual, e.g. figure 3.5.
> 
> One proper question to ask is at what point your protocol correctly models
> whatever relevant physical data exists that is relevant to what you want to
> observe. Drift that is too large is likely to affect observables, but will
> affect different ones differently.
> 
> Mark
> 
> On Fri, Sep 1, 2017 at 12:12 PM  wrote:
> 
>> Dear GROMACS Community,
>> 
>> I am trying to do a simulation using a tabulated potential which forces
>> me to use the group cut-off. I get a drift in the conserved quantity of
>> -600KJ/mol/ns. My system consists of 1000 rigid TIP4P water molecules
>> and a Na+ ion. I imagine that eventhough it will soon be deprecated the
>> group cutoff scheme still works correctly. I have tryed to change the
>> parameters without success and in any case the ones I use seem
>> reasonable (in my experience using other programs). The rdfs of the
>> system look normal so I ruled out topology problems.
>> 
>> It seems that the problem is in the group cut-off since
>> when I change the tabulated potential for a regular vdw the problem
>> persists. I have followed the instructions of:
>> 
>> http://www.gromacs.org/@api/deki/files/94/=gromacs_nb.pdf
>> 
>> to implement the tabulated potentials.
>> 
>> Is this the kind of energy drift acceptable? I have pasted a copy .mdp
>> 
>> Thanks for your help,
>> 
>> Sergio Perez-Conesa
>> 
>> integrator = md
>> dt = 0.001
>> nsteps = 10
>> init-step = 0
>> cutoff-scheme = group
>> nst-list = 1
>> verlet-buffer-tolerance = 0.0005
>> ns-type = grid
>> rlist = 1.3
>> pbc = xyz
>> coulombtype = PME-switch
>> rcoulomb = 1.
>> rcoulomb-switch = 0.95
>> pme-order = 4
>> fourierspacing = 0.1
>> ewald-rtol = 1.e-5
>> vdwtype = user
>> rvdw = 1.0
>> DispCorr = No
>> tcoupl = v-rescale
>> tc-grps = System
>> ;nsttcouple = 1
>> tau-t = ref-t = 300.0
>> constraints = all-angles
>> constraint-algorithm = LINCS
>> lincs_iter = 1
>> lincs_order = 4
>> energygrps = NA OW
>> energygrp_table = NA OW
>> comm-mode = linear
>> --
>> 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-requ...@gromacs.org.
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[gmx-users] Energy drift combining tabulated potentials and group cut-off.

[serpercon]

Dear GROMACS Community, 

I am trying to do a simulation using a tabulated potential which forces
me to use the group cut-off. I get a drift in the conserved quantity of
-600KJ/mol/ns. My system consists of 1000 rigid TIP4P water molecules
and a Na+ ion. I imagine that eventhough it will soon be deprecated the
group cutoff scheme still works correctly. I have tryed to change the
parameters without success and in any case the ones I use seem
reasonable (in my experience using other programs). The rdfs of the
system look normal so I ruled out topology problems.  

It seems that the problem is in the group cut-off since
when I change the tabulated potential for a regular vdw the problem
persists. I have followed the instructions of: 

http://www.gromacs.org/@api/deki/files/94/=gromacs_nb.pdf 

to implement the tabulated potentials. 

Is this the kind of energy drift acceptable? I have pasted a copy .mdp  

Thanks for your help, 

Sergio Perez-Conesa 

integrator = md 
dt = 0.001 
nsteps = 10 
init-step = 0 
cutoff-scheme = group 
nst-list = 1 
verlet-buffer-tolerance = 0.0005 
ns-type = grid 
rlist = 1.3 
pbc = xyz 
coulombtype = PME-switch 
rcoulomb = 1. 
rcoulomb-switch = 0.95 
pme-order = 4 
fourierspacing = 0.1 
ewald-rtol = 1.e-5 
vdwtype = user 
rvdw = 1.0 
DispCorr = No 
tcoupl = v-rescale 
tc-grps = System 
;nsttcouple = 1 
tau-t = ref-t = 300.0 
constraints = all-angles 
constraint-algorithm = LINCS 
lincs_iter = 1 
lincs_order = 4 
energygrps = NA OW 
energygrp_table = NA OW 
comm-mode = linear
-- 
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