OK. Thank you.
I will contact him.
Search found 14 matches
- Mon Apr 29, 2019 9:37 am
- Forum: OpenMM
- Topic: CHARMM FF LONEPAIR
- Replies: 4
- Views: 221
- Mon Apr 29, 2019 5:32 am
- Forum: OpenMM
- Topic: CHARMM FF LONEPAIR
- Replies: 4
- Views: 221
Re: CHARMM FF LONEPAIR
Sorry for confusing you. No, I am talking about CHARMM PSF parser. In wrappers/python/simtk/openmm/app/charmmpsffile.py line 374: https://github.com/pandegroup/openmm/blob/9b52307636fd735bfd9049a0b4c82085fd34f4e2/wrappers/python/simtk/openmm/app/charmmpsffile.py#L374 if numlp != 0 or numlph != 0: lp...
- Fri Apr 26, 2019 7:02 am
- Forum: OpenMM
- Topic: CHARMM FF LONEPAIR
- Replies: 4
- Views: 221
CHARMM FF LONEPAIR
Dear OpenMM developers,
It seems like that current OpenMM only supports 'relative' and 'bisector' types of LONEPAIR for Drude FF.
Do you have any plan to implement the support of 'COLINEAR' type LONEPAIR for CGenFF?
Best,
Jumin
It seems like that current OpenMM only supports 'relative' and 'bisector' types of LONEPAIR for Drude FF.
Do you have any plan to implement the support of 'COLINEAR' type LONEPAIR for CGenFF?
Best,
Jumin
- Mon Feb 11, 2019 8:14 am
- Forum: OpenMM
- Topic: Restraints with reference position changing based on system dimension
- Replies: 10
- Views: 665
Re: Restraints with reference position changing based on system dimension
Oh... The position of dummy atom may not be affected because mass is zero?
- Mon Feb 11, 2019 8:04 am
- Forum: OpenMM
- Topic: Restraints with reference position changing based on system dimension
- Replies: 10
- Views: 665
Re: Restraints with reference position changing based on system dimension
Thank you for the suggestion.
So, are you suggesting to use CustomBondForce?
However, if I apply a bond restraint between dummy and real atom, the position of dummy can be affected by the restraint force?
So, are you suggesting to use CustomBondForce?
However, if I apply a bond restraint between dummy and real atom, the position of dummy can be affected by the restraint force?
- Sat Feb 09, 2019 2:18 pm
- Forum: OpenMM
- Topic: Restraints with reference position changing based on system dimension
- Replies: 10
- Views: 665
Restraints with reference position changing based on system dimension
Dear OpenMM developers, Is there a way to construct a positional restraint with the reference position changing based on the system dimensions (in NPT ensemble)? For example, if I want to apply a restraint that maintains an atom at the center of a system, how should I construct the CustomExternalFor...
- Wed Jan 30, 2019 7:19 am
- Forum: OpenMM
- Topic: COM restraints using CustomCentroidBondForce
- Replies: 4
- Views: 203
Re: COM restraints using CustomCentroidBondForce
Thanks a lot!!
- Tue Jan 29, 2019 8:15 am
- Forum: OpenMM
- Topic: COM restraints using CustomCentroidBondForce
- Replies: 4
- Views: 203
Re: COM restraints using CustomCentroidBondForce
Thank you!
So, something like this?
So, something like this?
Code: Select all
force = CustomCentroidBondForce(2, "k(x1-x0)^2")
force.addPerBondParameter("k")
force.addPerBondParameter("x0")
force.addGroup(particles1)
force.addGroup(particles2)
force.addBond([0], [k, x0])
force.addBond([1], [k, x0])
- Mon Jan 28, 2019 1:00 pm
- Forum: OpenMM
- Topic: COM restraints using CustomCentroidBondForce
- Replies: 4
- Views: 203
COM restraints using CustomCentroidBondForce
Dear OpenMM developers, Is it possible to apply multiple COM restraints using a single CustomCentroidBondForce? For example, if I want to put two (or more) positional COM restraints at x=1 for group1 and x=10 for group2, do I need to construct two (or more) CustomCentroidBondForce for each? Thanks, ...
- Wed May 16, 2018 11:02 am
- Forum: OpenMM
- Topic: Constant Force
- Replies: 2
- Views: 151
Re: Constant Force
Thank you very much!
Best,
Jumin
Best,
Jumin