**From:** JC Gumbart (*gumbart_at_ks.uiuc.edu*)

**Date:** Fri May 03 2013 - 00:21:10 CDT

**Next message:**Norman Geist: "AW: Coarse-Grained fatal error!"**Previous message:**Peterson J: "Patching N- and C-Terms and their parameters"**Maybe in reply to:**Markus Dahlgren: "Re: dihedral parameter conversion"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

Good point! The negative force constants work in any case, although I just find it strange that they are so rare (but not completely absent!) in the standard charmm force field but are instead relatively prevalent in others. Thanks for your personal insight!

JC

On May 2, 2013, at 1:46 PM, Markus Dahlgren wrote:

*> Hi James,
*

*>
*

*> I just downloaded toppar_c36_aug12 from the mackerell groups homepage and looked at the file: par_all35_ethers.prm. There are terms with negative coefficients for the THP entry. I do not use CHARMM myself, but to me it is pretty obvious that the CHARMM force field has dihedral terms with negative coefficients, although maybe not many.
*

*>
*

*> -Markus
*

*>
*

*> On 5/2/2013 10:41 AM, JC Gumbart wrote:
*

*>> Do you use the negative coefficients in your charmm-formatted parameter file? There must be a reason though that the charmm force field has NO dihedral terms with negative coefficients. It seems like the two approaches are incompatible.
*

*>>
*

*>> I'll take a look at Dan Price's work to see if I can further sort it out.
*

*>>
*

*>> Thanks!
*

*>>
*

*>> -----Original Message-----
*

*>> From: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] On Behalf Of Markus Dahlgren
*

*>> Sent: Thursday, May 02, 2013 10:17 AM
*

*>> To: namd-l_at_ks.uiuc.edu
*

*>> Subject: Re: namd-l: dihedral parameter conversion
*

*>>
*

*>> There is an OPLS parameter file that Dan Price prepared using the program PEPZ that is output in the CHARMM format. The fourier coefficients are the OPLS coefficients divided by 2. So a V1 of -5 would be -2.5.
*

*>>
*

*>> You also have to convert sigma and epsilon for all atom types.
*

*>>
*

*>> I have run several NAMD simulations using OPLS and I have checked dihedral distributions generated with NAMD and compared it with MP2 dihedral profiles that parameters were fitted against and it looks correct. OPLS and CHARMM have very similar formats. The main difference is the absence of CMAP in OPLS.
*

*>>
*

*>> -Markus
*

*>>
*

*>> On 5/2/2013 9:17 AM, JC Gumbart wrote:
*

*>>> I'm not so familiar with the formats of force fields other than CHARMM, but I want to convert one for OPLS to CHARMM-style for running in NAMD. The main issue I've yet to resolve though is the format of the dihedrals. Here's an example line from the original parameter file:
*

*>>>
*

*>>> ; ai aj ak al funct ; Amber type OPLS type Type V1 V2 V3 Comments
*

*>>> 1 4 5 6 3 -0.50208 -1.50624 0.00000 2.00832 0.000 0.000 ; C3-N3-C2-C2 4031-4030-4032-4004 5000 0.000 0.000 -0.240
*

*>>>
*

*>>> I realize the first part is an RB format. The second part, I guess (please correct me if I'm wrong!!!), uses this functional form:
*

*>>>
*

*>>> V(φ) =V1(1+ cosφ)/2+V2(1−cos2φ)/2+V3(1+ cos3φ)/2+V4(1−cos4φ)/2
*

*>>>
*

*>>> So for the example line, the potential would be V = -0.12*(1+cos(3*phi)). But how to represent this in CHARMM??? Because it can't be JUST a phase shift, then we would have V = 0.12*(1+cos(3*phi-180)) = 0.12*(1-cos(3*phi)). In other words, there is a constant shift in the potential energy equal to V3.
*

*>>>
*

*>>> What simple fact am I misunderstanding here? How does one convert force constants less than zero to charmm, where they are always greater than zero?
*

*>>>
*

*>>> Thanks!
*

*>>> JC
*

*>>>
*

**Next message:**Norman Geist: "AW: Coarse-Grained fatal error!"**Previous message:**Peterson J: "Patching N- and C-Terms and their parameters"**Maybe in reply to:**Markus Dahlgren: "Re: dihedral parameter conversion"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

*
This archive was generated by hypermail 2.1.6
: Wed Dec 31 2014 - 23:21:10 CST
*