Andrew DeYoung wrote:
Justin,
Thank you so much for your help! That was really helpful.
It seems that I simply append my [ nonbond_params ] section to the end of my
ffnonbonded.itp file. However, if I ONLY have this:
---
; ffnonbonded.itp
[ atomtypes ]
;type at.n mass charge ptype sig eps
; all of the liquid atomtypes
; ...
[ nonbond_params ]
; i j func sig eps
mywall N 1 0.29750 4.56912
mywall C 1 0.31200 3.07524
mywall H 1 0.26170 1.17675
mywall B 1 0.31225 3.48667
mywall F 1 0.28974 2.82420
---
then I get an error message saying that atomtype mywall does not exist.
However, if I simply add a bogus entry for mywall in the [ atomtypes ]
section of ffnonbonded.itp, then grompp runs fine:
Right, you can't use an atomtype unless it is defined.
---
; ffnonbonded.itp
[ atomtypes ]
;type at.n mass charge ptype sig eps
mywall 6 12.01100 0.000 A 0.00000e-1 0.00000e-1 ; bogus sig and eps
; all of the liquid atomtypes
; ...
[ nonbond_params ]
; i j func sig eps
mywall N 1 0.29750 4.56912
mywall C 1 0.31200 3.07524
mywall H 1 0.26170 1.17675
mywall B 1 0.31225 3.48667
mywall F 1 0.28974 2.82420
---
Is there any way that I can verify that the code is actually using the
parameters for mywall in the [ nonbond_params ] section, rather than the
bogus parameters (0 for sig and eps) for mywall in the [ atomtypes ]
section?
Run gmxdump on your .tpr file. All the relevant parameters should be in there
somewhere.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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