[gmx-users] table-extension distance appears to be over-ridden by .mdp file cut-off values

Elizabeth Ploetz ploetz at ksu.edu
Fri Dec 20 18:56:15 CET 2013 

Hi Justin,

Something along these lines would have been useful to me:

Addition to a sentence from Section 6.9.2 User-specified potential functions:
"...The x should run from 0 to rc + 1 (the value of table-extension can be changed in the .mdp file), 
but the value of table-extension and the length of the table does not effect the length of the cutoff applied to the tabulated potentials..."

Section 7.3.10 Electrostatics:
coulombtype:
User
"...For the non-bonded interactions x values should run from 0 to the largest cut-off distance + table-extension and should be uniformly spaced..."
Add: "Note that the value of table-extension will not effect the cut-offs, which will be taken from rlist and rcoul in the .mdp file."

Another small side-comment (Still Electrostatics > coulombtype > User) 
It says, "More information is in the printed manual." This sentence could be removed from the printed manual. 
Or "elsewhere" could be inserted, if that was the intent.

table-extension: (1) [nm]
Extension of the non-bonded potential lookup tables beyond the largest cut-off distance. The
value should be large enough to account for charge group sizes and the diffusion between
neighbor-list updates. Without user defined potential the same table length is used for the
lookup tables for the 1-4 interactions, which are always tabulated irrespective of the use of
tables for the non-bonded interactions. 
Add: "Note that the value of table-extension will not effect the cut-offs."

energygrp-table:
When user tables are used for electrostatics and/or VdW, here one can give pairs of energy
groups for which seperate user tables should be used. The two energy groups will be appended
to the table file name, in order of their definition in energygrps, seperated by
underscores. For example, if energygrps = Na Cl Sol and energygrp-table
= Na Na Na Cl, mdrun will read table_Na_Na.xvg and table_Na_Cl.xvg in
addition to the normal table.xvg which will be used for all other energy group pairs.
Add: "Note that different cut-offs for different energy group pairs is not a supported feature of Gromacs."

Elizabeth
________________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Justin Lemkul <jalemkul at vt.edu>
Sent: Friday, December 20, 2013 11:21
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] table-extension distance appears to be over-ridden by .mdp file cut-off values

On 12/20/13 12:09 PM, ploetz wrote:
> Hi Justin,
>
> Thanks for your reply. I agree with you that the .mdp file rlist=rcoul=rvdw cutoff is really being applied,
> but the documentation in the manual about tabulated interaction functions does not
> give me the impression that that is the intent. It reads like the user can have different cut-offs
> by using table-extension (below).
>

Could you suggest how the text might be improved?  Reading through it a couple
of times, I still don't see how one would assume different cutoffs could be used
for different interactions.  Different potentials, yes, because you can tabulate
whatever you like, but the values of the cutoffs are always fixed.  Of course, I
am reading through the text knowing already how it works, so my interpretation
may be different.  Suggestions on improvements are always welcome, especially in
the case of clarity!

-Justin

> Elizabeth
> -----
>
> 6.9.2 User-specified potential functions
>
> You can also use your own s without editing the GROMACS code. The potential function should
>
> be according to the following equation V(rij)=[qiqj/(4pi*epsilon0)]f(rij)+C6g(rij)+C12h(rij) (6.75)
>
> where f, g, and h are user defined functions. Note that if g(r) represents a normal dispersion
>
> interaction, g(r) should be < 0. C6, C12 and the charges are read from the topology. Also note
>
> that combination rules are only supported for Lennard-Jones and Buckingham, and that your tables
>
> should match the parameters in the binary topology.
>
> When you add the following lines in your .mdp file:
>
> rlist = 1.0
>
> coulombtype = User
>
> rcoulomb = 1.0
>
> vdwtype = User
>
> rvdw = 1.0
>
> mdrun will read a single non-bonded table file, or multiple when energygrp-table is set (see
>
> below). The name of the file(s) can be set with the mdrun option -table. The table file should
>
> contain seven columns of table look-up data in the order: x, f(x), -f'(x), g(x), -g'(x), h(x),
>
> -h'(x). The x should run from 0 to rc + 1 (the value of table_extension can be changed
>
> in the .mdp file). You can choose the spacing you like; for the standard tables GROMACS uses a
>
> spacing of 0.002 and 0.0005 nm when you run in single and double precision, respectively. In this
>
> context, rc denotes the maximum of the two cut-offs rvdw and rcoulomb (see above). These
>
> variables need not be the same (and need not be 1.0 either). Some functions used for potentials
>
> contain a singularity at x = 0, but since atoms are normally not closer to each other than 0.1 nm,
>
> the function value at x = 0 is not important. Finally, it is also possible to combine a standard
>
> Coulomb with a modified LJ potential (or vice versa). One then specifies e.g. coulombtype =
>
> Cut-off or coulombtype = PME, combined with vdwtype = User. The table file must
>
> always contain the 7 columns however, and meaningful data (i.e. not zeroes) must be entered in
>
> all columns. A number of pre-built table files can be found in the GMXLIB directory for 6-8, 6-9,
>
> 6-10, 6-11, and 6-12 Lennard-Jones potentials combined with a normal Coulomb.
>
> If you want to have different functional forms between different groups of atoms, this can be set
>
> through energy groups. Different tables can be used for non-bonded interactions between different
>
> energy groups pairs through the .mdp option energygrp-table (see sec. 7.3). Atoms that
>
> should interact with a different potential should be put into different energy groups. Between
>
> group pairs which are not listed in energygrp-table, the normal user tables will be used.
>
> This makes it easy to use a different functional form between a few types of atoms.
>
>
> Also:
>
> 7.3.10 Electrostatics
>
> coulombtype:
>
> User
>
> mdrun will now expect to find a file table.xvg with user-defined potential functions
>
> for repulsion, dispersion and Coulomb. When pair interactions are present,
>
> mdrun also expects to find a file tablep.xvg for the pair interactions. When the
>
> same interactions should be used for non-bonded and pair interactions the user can
>
> specify the same file name for both table files. These files should contain 7 columns:
>
> the x value, f(x), -f’(x), g(x), -g’(x), h(x), -h’(x), where f(x) is the
>
> Coulomb function, g(x) the dispersion function and h(x) the repulsion function.
>
> When vdwtype is not set to User the values for g, -g’, h and -h’ are ignored. For
>
> the non-bonded interactions x values should run from 0 to the largest cut-off distance
>
> + table-extension and should be uniformly spaced. For the pair interactions the
>
> table length in the file will be used. The optimal spacing, which is used for non-user
>
> tables, is 0.002 [nm] when you run in single precision or 0.0005 [nm] when you
>
> run in double precision. The function value at x=0 is not important. More information
>
> is in the printed manual.
>
>
> 7.3.11 VdW
>
> vdwtype:
>
> User
>
> See user for coulombtype. The function value at x=0 is not important. When
>
> you want to use LJ correction, make sure that rvdw corresponds to the cut-off in the
>
> user-defined function. When coulombtype is not set to User the values for f and
>
> -f’ are ignored.
>
>
> 7.3.12 Tables
>
> table-extension: (1) [nm]
>
> Extension of the non-bonded potential lookup tables beyond the largest cut-off distance. The
>
> value should be large enough to account for charge group sizes and the diffusion between
>
> neighbor-list updates. Without user defined potential the same table length is used for the
>
> lookup tables for the 1-4 interactions, which are always tabulated irrespective of the use of
>
> tables for the non-bonded interactions.
>
> energygrp-table:
>
> When user tables are used for electrostatics and/or VdW, here one can give pairs of energy
>
> groups for which seperate user tables should be used. The two energy groups will be appended
>
> to the table file name, in order of their definition in energygrps, seperated by
>
> underscores. For example, if energygrps = Na Cl Sol and energygrp-table
>
> = Na Na Na Cl, mdrun will read table_Na_Na.xvg and table_Na_Cl.xvg in
>
> addition to the normal table.xvg which will be used for all other energy group pairs.
>
> ________________________________
> From: Justin Lemkul [via GROMACS] <ml-node+s5086n5013404h97 at n6.nabble.com>
> Sent: Wednesday, December 18, 2013 20:23
> To: Elizabeth Ploetz
> Subject: Re: table-extension distance appears to be over-ridden by .mdp file cut-off values
>
>
> Caveat to start: I am not an expert on tabulated potentials, but I'll take a
> crack at helping in case it inspires a solution :)
>
> Very thorough report, so thanks for providing an exemplary level of detail.
>
> On 12/18/13 3:39 PM, Elizabeth Ploetz wrote:
>
>> Dear Gromacs Users,
>>
>> I'm trying to use tabulated VdW potentials that are non-zero until image-distance/2.0, but they seem to be over-ridden by the cut-offs in the .mdp file. I'm hoping someone with experience with the use of tabulated potentials plus the table-extension .mdp file option can tell me if I have not made all of the necessary changes so that the tables are correctly implemented. Here are the details of what I've done.
>>
>> I have five systems each consisting of a single Lennard-Jones (6-12) sphere in TIP3P water (rhombic dodecahedron, 15nm image-distance for each system). The Lennard-Jones parameters for the infinitely-dilute LJ-sphere are as follows:
>> System Sigma (nm) Epsilon (kJ/mol)
>> 1             0.3             0.1
>> 2             1.5             0.1
>> 3             3.0             0.1
>> 4             4.5             0.1
>> 5             6.0             0.1
>> For each system, rlist=rvdw=rcoulomb=0.8 (nm). vdw-type=User, coulombtype=PME, table-extension=6.7 (nm). 6.7 nm was chosen because 6.7nm+0.8nm=7.5nm=half the image-distance. A tabulated potential is only used so that the LJ-sphere - water interactions can have a different (larger) cut-off than the water-water interactions since the sigma/2.0 values for the LJ-sphere are greater than the 0.8 nm cut-off for Systems 3-5.
>>
>
> I'm not sure I follow the logic here.  The value of table-extension does not
> give you a special cutoff, per se.
>
>> When I run these systems (version 4.6), the LJ-sphere-to-water center-of-mass RDFs look correct for Systems 1 and 2 (the two LJ-spheres that have a radius less than the rlist=rvdw=rcoulomb cut-off). The RDFs look "wrong" for all larger spheres, and worse and worse as the Lennard-Jones sigma values increase. By "wrong," I mean that the RDFs take on positive values at too short of radial distances (i.e., water is being "sucked in" too close to the Lennard-Jones sphere). This makes sense if my tabulated VdW-potentials are not really being used (or, equivalently, not being used beyond 0.8 nm), and consequently the waters do not "see" the LJ-sphere until they are <0.8 nm away from the sphere. The simulations for the larger LJ-spheres are also unstable, which would also make sense, because waters that could get so close to the sphere would be well within the repulsive region of the sphere-to-water potential once they finally suddenly "saw" the sphere at <0.8 nm. The types of er!
 r!
>   ors I get
> when the systems crash (usually after around 20 ps) are domain decomposition errors, specifically:
>
>>
>> Fatal error:
>> A charge group moved too far between two domain decomposition steps
>> This usually means that your system is not well equilibrated
>> For more information and tips for troubleshooting, please check the GROMACS
>> website at http://www.gromacs.org/Documentation/Errors
>>
>> Or (when I change to particle-decomposition or use only one processor), the simulations eventually crash due to LINCS.
>>
>> The details of my .mdp file and tabulated potentials are below my signature, as well as an example of the .log file output.
>>
>> Have I missed any extra flags that need to be defined so that the tabulated potentials are really used [the .log file output suggests they are really being used and so does mdrun.debug (not attached, but I can provide)]? Or, does anyone know of a way to check whether or not the tabulated potentials are really being used up to the cut-off + table-extension and not just up to the cut-off?
>>
>> Please note that, as a test, I did a series of energy minimizations on a simpler system, the Lennard-Jones sphere (sigma = 6 nm) and a single water molecule, when varying the coordinates of the water molecule systematically between 7.5 nm and 0.3 nm away from the LJ-sphere. The LJ(SR) sphere-water potential energy was zero for all distances except when the water molecule was < 0.8 nm from the LJ-sphere. This, again, indicates that the rlist=rcoul=rvdw=0.8 nm cut-off distance is being used for the sphere-water interactions instead of the extended distance.
>>
>
> I think we need to clarify a bit about what those settings are doing.  The value
> of table-extension does not give you some special value of cutoff for different
> interactions.  It is used to keep track of interactions beyond the cutoff
> between neighborlist updates.  I think your observations are consistent with a
> 0.8-nm cutoff, beyond which the energy is zero.
>
> It seems to me that, given the LJ parameters above, as soon as any water
> molecule moves within 0.8 nm of the LJ sphere in system 5, the potential will
> spike to +1 billion kJ/mol or thereabouts, and the system will crash.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> [hidden email]</user/SendEmail.jtp?type=node&node=5013404&i=0> | (410) 706-7441
>
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--
==================================================

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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