Hi ! >
I am trying to reproduce results from reported polyacrylate simulations from literature. I have the values for bonded and non-bonded interaction parameters along with the the charges on atoms. I edited the charges and charge groups in the itp file. I would like to know whether in the [bonds } section, I can edit the itp file and give the force constants for the bonds instead of the non-bonded force constants (which the PRODRG provides). Similar edting for the angles and dihedrals sections would make the itp file suitable for running MD simulations. I ran MD simaultions with the existing itp file (with just editing the charges) , but simulation results were not comapring favorably with the reported values). I also would like to know, in the top file, #include ffg43a1.itp #include paa.itp the order should be as given above, or the reverse #include paa.itp #include ffg43a1.itp I read from the manual that, if any parameters are eneterd twice, the values which are read the second time will be taken. In addition, I read FAQ for PRODRG, but was of no help in trying to understand the details of the ff parameters in the itp file it generates. >From where I can get the information on the details of itp file generated by PRODRG. Thanking you for any help, Sulatha > Mark Abraham wrote: > >> On 03/02/10 15:55, sulatha M. S wrote: >> >>> Dear gromas users, >>> I am new to gromacs and trying to run polyacrylate MD simulation. I >>> obtained an itp file using PRODRG (gromos 96 force-field parameters). >>> When I compare with the same forcefield parameters in the gromacs/top >>> directory, they are far too off. For eg. >>> >>> [ bonds ] >>> ; ai aj fu c0, c1, ... >>> 2 1 2 0.125 13400000.0 0.125 13400000.0 ; CAC OAD >>> 2 3 2 0.125 13400000.0 0.125 13400000.0 ; CAC OAE >>> 4 2 2 0.153 7150000.0 0.153 7150000.0 ; CAB CAC >>> 4 5 2 0.153 7150000.0 0.153 7150000.0 ; CAB CAA >>> 4 6 2 0.153 7150000.0 0.153 7150000.0 ; CAB CAG >>> 7 6 2 0.153 7150000.0 0.153 7150000.0 ; CAH CAG >>> 7 8 2 0.153 7150000.0 0.153 7150000.0 ; CAH CAI >>> >>> As I understand, the function type should be 1 and c1 values should >>> correspond to the force constant for bond stretching. But here it >>> corresponds to the pair wise non bond parameters as listed in the >>> gromacs/top force-field file. Similarly, >>> >> >> The bonded function type can have a whole range of values. See table in >> section 5.7.1 of the manual. That and the parameters, and the form of the >> target forcefield have to be considered as a whole in judging acceptability. >> >> It's quite conceivable that the same numerical values are used in a bonded >> interaction (in [bonds] above) and forming the parameters in non-bonded >> interaction (in the [atomtypes] in the ffG96XXXbon.itp file) for in this >> case both pairs can represent quantities whose dimensions are length and >> energy respectively. >> >> [ pairs ] >>> ; ai aj fu c0, c1, ... >>> 1 5 1 ; OAD CAA >>> 1 6 1 ; OAD CAG >>> 2 7 1 ; CAC CAH >>> 3 5 1 ; OAE CAA >>> 3 6 1 ; OAE CAG >>> 4 8 1 ; CAB CAI >>> 4 11 1 ; CAB CAL >>> 5 7 1 ; CAA CAH >>> >>> there are no pair terms listed here in the pairs section. >>> >> >> Some forcefields generate these solely from the [atomtype] data. >> >> [ angles ] >>> ; ai aj ak fu c0, c1, ... >>> 1 2 3 2 126.0 770.0 126.0 770.0 ; OAD CAC OAE >>> 1 2 4 2 117.0 635.0 117.0 635.0 ; OAD CAC CAB >>> 3 2 4 2 117.0 635.0 117.0 635.0 ; OAE CAC CAB >>> 2 4 5 2 109.5 520.0 109.5 520.0 ; CAC CAB CAA >>> 2 4 6 2 109.5 520.0 109.5 520.0 ; CAC CAB CAG >>> 5 4 6 2 109.5 520.0 109.5 520.0 ; CAA CAB CAG >>> 4 6 7 2 109.5 520.0 109.5 520.0 ; CAB CAG CAH >>> For angles also the fu term is 2 instead of 1, although the angle and >>> the force constant parameters are correct. >>> >>> Similar errors are there in the dihedrals section also. >>> >>> This means I need to almost fully edit the itp file I got from PRODRG to >>> proceed further. Thank you in advance for any help and please clarify >>> whether the itp file from PRODRG is unreliable even while using GROMOS96 >>> force field ? >>> >> >> There's no evidence of any error here. You should satisfy yourself from >> the contents of chapter 5 and the correct form of the GROMOS energy function >> that PRODRG is doing what you think it should. It looks to me like PRODRG is >> fine and you don't yet understand the form of what it should be producing. I >> suggest that you should do that learning. >> >> Whether the numerical values will be sensible for MD simulations (as >> distinct from being expressed in a suitable form) is quite another question. >> > > And in addition, the most problematic section of a PRODRG topology is the > [atoms] - the charges and charge groups are often unsatisfactory, requiring > manual adjustment and validation (as you should, anyway, but the face-value > parameters are often inconsistent with the original force field). > > -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 > > ======================================== > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
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