[gmx-users] Trying to add Buck.ham (SR) while the default nonbond type is LJ (SR)
Andreas Mecklenfeld
a.mecklenfeld at tu-braunschweig.de
Fri Aug 12 16:09:29 CEST 2016
Dear Mark and Justin,
I've switched to function type 1 and the simulation runs. I thought the
function type would correspond to the type of the comb-rule and missed
the information given in the 5.8.1 section of the manual.
Thanks a lot!
Andreas
Am 12.08.2016 um 14:15 schrieb Justin Lemkul:
>
>
> On 8/12/16 8:11 AM, Andreas Mecklenfeld wrote:
>> Hello Mark,
>>
>> sorry for the confusion I've created. My system refers to a solute in
>> water
>> (which has only LJ-parameters for the oxygen atom). Within the
>> solute, there are
>> two approaches to deal with LJ-interactions:
>>
>> 1) intramolecular interactions (including 1-4 and far-off interactions)
>> 2) intermolecular interactions with the oxygens of ambient water
>>
>> There are certain atom types, which handle points 1) and 2) with
>> different sets
>> of LJ-parameters. Since the water oxygen is not included within the
>> solute
>> topology, the pair potential between the affected solute atomtype and
>> the
>> water-oxygen atomtype therefore has to be intermolecular.
>>
>> My .top file looks like this:
>>
>> #########################################################################################################
>>
>>
>>
>> [ defaults ]
>> ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
>> 1 2 yes 0.5 0.8333
>>
>> [ atomtypes ]
>> ;name bond_type mass charge ptype sigma epsilon Amb
>> o3 o3 0.00000 0.00000 A 2.95992e-01
>> 8.78640e-01 ; 1.66
>> 0.2100
>> oa oa 0.00000 0.00000 A 3.06647e-01
>> 8.80314e-01 ; 1.72
>> 0.2104
>> od od 0.00000 0.00000 A 2.95992e-01
>> 8.78640e-01 ; 1.66
>> 0.2100
>> nd nd 0.00000 0.00000 A 3.25000e-01
>> 7.11280e-01 ; 1.82
>> 0.1700
>> nl nl 0.00000 0.00000 A 3.25000e-01
>> 7.11280e-01 ; 1.82
>> 0.1700
>> sh sh 0.00000 0.00000 A 3.56359e-01
>> 1.04600e+00 ; 2.00
>> 0.2500
>> o3i o3i 0.00000 0.00000 A 0.331503 0.878640 ;
>> 1.66 0.2100
>> oai oai 0.00000 0.00000 A 0.295778 0.880314 ;
>> 1.72 0.2104
>> odi odi 0.00000 0.00000 A 0.320724 0.878640 ;
>> 1.66 0.2100
>> ndi ndi 0.00000 0.00000 A 0.349232 0.711280 ;
>> 1.82 0.1700
>> nli nli 0.00000 0.00000 A 0.299003 0.711280 ;
>> 1.82 0.1700
>> shi shi 0.00000 0.00000 A 0.334978 1.046000 ;
>> 2.00 0.2500
>> c3 c3 0.00000 0.00000 A 3.39967e-01
>> 4.57730e-01 ; 1.91
>> 0.1094
>> hc hc 0.00000 0.00000 A 2.64953e-01
>> 6.56888e-02 ; 1.49
>> 0.0157
>> c c 0.00000 0.00000 A 3.39967e-01
>> 3.59824e-01 ; 1.91
>> 0.0860
>> o o 0.00000 0.00000 A 2.95992e-01
>> 8.78640e-01 ; 1.66
>> 0.2100
>> n n 0.00000 0.00000 A 3.25000e-01
>> 7.11280e-01 ; 1.82
>> 0.1700
>> hn hn 0.00000 0.00000 A 1.06908e-01
>> 6.56888e-02 ; 0.60
>> 0.0157
>> cc cc 0.00000 0.00000 A 3.39967e-01
>> 3.59824e-01 ; 1.91
>> 0.0860
>> cd cd 0.00000 0.00000 A 3.39967e-01
>> 3.59824e-01 ; 1.91
>> 0.0860
>> h4 h4 0.00000 0.00000 A 2.51055e-01
>> 6.27600e-02 ; 1.41
>> 0.0150
>> h5 h5 0.00000 0.00000 A 2.42146e-01
>> 6.27600e-02 ; 1.36
>> 0.0150
>> na na 0.00000 0.00000 A 3.25000e-01
>> 7.11280e-01 ; 1.82
>> 0.1700
>> h1 h1 0.00000 0.00000 A 2.47135e-01
>> 6.56888e-02 ; 1.39
>> 0.0157
>> ss ss 0.00000 0.00000 A 3.56359e-01
>> 1.04600e+00 ; 2.00
>> 0.2500
>> ca ca 0.00000 0.00000 A 3.39967e-01
>> 3.59824e-01 ; 1.91
>> 0.0860
>> ha ha 0.00000 0.00000 A 2.59964e-01
>> 6.27600e-02 ; 1.46
>> 0.0150
>> oh oh 0.00000 0.00000 A 3.06647e-01
>> 8.80314e-01 ; 1.72
>> 0.2104
>> ho ho 0.00000 0.00000 A 0.00000e+00
>> 0.00000e+00 ; 0.00
>> 0.0000
>> HW_tip4pew 1 1.008 0.0000 A 0.00000e+00 0.00000e+00
>> OW_tip4pew 8 16.00 0.0000 A 3.16435e-01 6.80946e-01
>> MW 0 0.0000 0.0000 D 0.00000e+00 0.00000e+00
>>
>> [ nonbond_params ]
>> OW_tip4pew o3i 2 0.323969 0.773503
>> OW_tip4pew oai 2 0.306107 0.774239
>> OW_tip4pew odi 2 0.318579 0.773503
>> OW_tip4pew ndi 2 0.332834 0.695948
>> OW_tip4pew nli 2 0.307719 0.695948
>> OW_tip4pew shi 2 0.325706 0.843961
>>
>>
>>
>> #include "Asn.itp"
>> #include "tip4pew.itp"
>>
>>
>>
>> [ system ]
>> Asn in tip4pew
>>
>>
>> [ molecules ]
>> ; molecule name nr.
>> Asn 1
>> SOL 900
>>
>>
>>
>> #########################################################################################################
>>
>>
>>
>> When I comment out the [ non_bond_params ] section, everything works
>> fine, thus
>> I would locate the error to this point.
>> The error I receive is actually the one from the mail subject:
>>
>> ERROR 1 [file topol.top, line 44]:
>> Trying to add Buck.ham (SR) while the default nonbond type is LJ (SR)
>>
>> followed by repetitions regarding the other lines in the [
>> non_bond_params ]
>> section.
>>
>
> You have specified type 2 for the [ nonbond_params ] section, which
> corresponds to Buckingham. If you want normal LJ, set the type field
> to 1.
>
> -Justin
>
>>
>>
>> Thanks for your help!
>> Andreas
>>
>>
>>
>>
>>
>> Am 12.08.2016 um 09:49 schrieb Mark Abraham:
>>> Hi,
>>>
>>> On Fri, Aug 12, 2016 at 9:16 AM Andreas Mecklenfeld <
>>> a.mecklenfeld at tu-braunschweig.de> wrote:
>>>
>>>> Hello Mark,
>>>>
>>>> thanks for the reply. The point is, I don't.
>>>
>>> Ah, I read your original email more closely now. The use of a
>>> subject line
>>> that reflected your error message rather than your intention
>>> confused me.
>>>
>>>
>>>> I found some Lennard-Jones
>>>> parametrization in literature that distinguishes between intra- and
>>>> intermolecular (oxygen atom of water) interactions.
>>>
>>> Um, typical water models have no intra-molecular LJ interactions.
>>>
>>>
>>>> My intention was
>>>> thus to define the specific eps_ij and sigma_ij for the corresponding
>>>> atomtypes, which I thought should be dealt with in the [
>>>> nonbond_params
>>>> ] section. All parameters are for Lennard-Jones and this is the
>>>> potential I want to use. I have no idea why the usage of Buckingham is
>>>> assumed. I'm using Gromacs 5.1 btw.
>>>>
>>> Then somewhere (e.g. [nonbond_params]) you are using a number that
>>> is being
>>> interpreted as a function type that is Buckingham, which of course
>>> makes no
>>> sense for a code that assumes each atom type has at most one set of LJ
>>> parameters. But we haven't seen your full topology or full error
>>> message.
>>>
>>> Mark
>>>
>>>
>>>> Thanks,
>>>> Andreas
>>>>
>>>>
>>>>
>>>> Am 11.08.2016 um 17:59 schrieb Mark Abraham:
>>>>> Hi,
>>>>>
>>>>> How do you want your atoms with lj parameters to interact with
>>>>> atoms with
>>>>> Buckingham parameters?
>>>>>
>>>>> Mark
>>>>>
>>>>> On Fri, 5 Aug 2016 08:53 Andreas Mecklenfeld <
>>>>> a.mecklenfeld at tu-braunschweig.de> wrote:
>>>>>
>>>>>> Dear Gromacs-users,
>>>>>>
>>>>>> I'm trying to modify some intermolecular Lennard-Jones interactions
>>>>>> based on the GAFF force field. I've altered the topology file
>>>>>> according
>>>> to
>>>>>>
>>>>>>
>>>> ############################################################################
>>>>
>>>>>> [ defaults ]
>>>>>> ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
>>>>>> 1 2 yes 0.5 0.8333
>>>>>>
>>>>>> [ atomtypes ]
>>>>>> ...
>>>>>>
>>>>>> [ nonbond_params ]
>>>>>> type1 type2 sigma epsilon
>>>>>> ...
>>>>>>
>>>>>> #include ...
>>>>>>
>>>>>> [ system ]
>>>>>> ...
>>>>>>
>>>>>> [ molecules ]
>>>>>> ...
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>> ############################################################################
>>>>
>>>>>> Sigma and epsilon for atoms type1 and type2 are calculated
>>>>>> according to
>>>>>> the Lorentz-Berthelot combination rule. The error I receive is
>>>>>>
>>>>>> "Trying to add Buck.ham (SR) while the default nonbond type is LJ
>>>>>> (SR)",
>>>>>> though I obviously want to use LJ and did not intentionally set
>>>>>> any flag
>>>>>> for Buckingham. Is there any way to fix this?
>>>>>>
>>>>>> Cheers,
>>>>>>
>>>>>> Andreas
>>>>>>
>>>>>>
>>>>>> --
>>>>>> M. Sc. Andreas Mecklenfeld
>>>>>> Stipendiat
>>>>>>
>>>>>> Technische Universität Braunschweig
>>>>>> Institut für Thermodynamik
>>>>>> Hans-Sommer-Straße 5
>>>>>> 38106 Braunschweig
>>>>>> Deutschland / Germany
>>>>>>
>>>>>> Tel: +49 (0)531 391-2634
>>>>>> Fax: +49 (0)531 391-7814
>>>>>>
>>>>>> http://www.ift-bs.de
>>>>>>
>>>>>> --
>>>>>> 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
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>>>>>> or
>>>>>> send a mail to gmx-users-request at gromacs.org.
>>>> --
>>>> M. Sc. Andreas Mecklenfeld
>>>> Stipendiat
>>>>
>>>> Technische Universität Braunschweig
>>>> Institut für Thermodynamik
>>>> Hans-Sommer-Straße 5
>>>> 38106 Braunschweig
>>>> Deutschland / Germany
>>>>
>>>> Tel: +49 (0)531 391-2634
>>>> Fax: +49 (0)531 391-7814
>>>>
>>>> http://www.ift-bs.de
>>>>
>>>> --
>>>> 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
>>>>
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>>
>
--
M. Sc. Andreas Mecklenfeld
Stipendiat
Technische Universität Braunschweig
Institut für Thermodynamik
Hans-Sommer-Straße 5
38106 Braunschweig
Deutschland / Germany
Tel: +49 (0)531 391-2634
Fax: +49 (0)531 391-7814
http://www.ift-bs.de
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