[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 14:11:15 CEST 2016
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.
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
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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
>>
>> --
>> 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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