Hello all, It seems I'm still getting errors when doing a FEP on a molecule (a -CH3 to a -H). This below is for when I was charging things from a -H uncharged to -H charged, although it also happens when I'm actually converting the -CH3 to -H (at Lambdas greater than 85%). I made sure to keep the charges balanced at 0 while mutating and I did it at 3 steps like Michael Shirts suggested.
Set 1: turn R-CH3 charges off in a way that preserves the total charge. Set 2: change CH3 LJ to H LJ Set 3: Turn R-H charges on in a way that preserves the total charge. In the portion of the error below atom 9 is -C9-(H67,H68,H66) which in this specific case H67 is already a dummy molecule with no mass or charge. From what I can see, it seems that the atoms do not know how to treat the dummy molecules in terms of angles. How should I treat the dummy molecules? Should I be treating them like hollow spheres with no charge so I would assign them angle constraints? I think it can also be that I'm peturbing the dihedral angles incorrectly. I received errors at first saying that dihedral multiplicities can't be peturbed so I had to equal the multiplicities just to get it to run. Does anybody have any experience with this? Thank you for your help. -Fabian Casteblanco Portion of Error Output: ----------------------------------------------------------------- Reading file nvt0.5.tpr, VERSION 4.5.3 (single precision) starting mdrun 'SIMVASTATIN' 150000 steps, 300.0 ps. Step 7, time 0.014 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.006111, max 0.139443 (between atoms 9 and 67) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length Step 8, time 0.016 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.007341, max 0.167622 (between atoms 9 and 67) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length Step 8, time 0.016 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.008771, max 0.201182 (between atoms 9 and 67) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length > On Mon, Oct 10, 2011 at 4:10 PM, Fabian Casteblanco > <fabian.castebla...@gmail.com> wrote: >> Hi all, >> >> I have an additional question related to what Steven Neumann was >> mentioning. I actually have to do a molecule mutation. I'm trying to >> use Michael Shirts method 1) making small >> changes 'alchemical' changes in the molecules and computing the free >> energies by any method (BAR, TI, etc). I'm specifically want to try >> to use BAR at the end once I collect all the data. This helped a lot >> on clarification since it seemed that Justin's tutorial is essentially >> a FEP except its using the BAR mathematical method for computing the >> complete decoupling of the molecule rather than using the old FEP >> mathematics of the exponential averaging formula. So BAR is only >> referring to the mathematical code used to calculate the overall free >> energy for the FEP, correct? >> >> My question is, for a mutation of a -CH3 group to a -H group, is it >> better to simply run: >> [+ from (Lambda=0 , R-CH3, full charges and interactions -STATE A) >> --> (Lambda=1, R-CH, full charges and interactions -STATE B)] >> >> OR >> >> [1) from (Lambda=0 , R-CH3, STATE A : Charges and LJ Interactions: ON) >> 2) (Lambda=?, -CH3 Charges: OFF ,LJ Interactions: ON and unmutated) >> 3) (Lambda=?, R-CH3, -CH3 Charges: OFF ,LJ Interactions: OFF) >> 4) (Lambda=?, R-CH3, -CH3 Charges: OFF ,LJ interactions: ON and Mutated to >> -H) >> 5) (Lambda=1, R-CH3, -CH3 STATE B : Charges and LJ Interactions: ON) >> >> Reason I'm asking is because when I try the first choice to do it >> STATE A to STATE B in one step, when I reach Lambda=0.85 and above on >> the NVT equilibration right after EM, I receive errors saying that >> bonds are moving way to far off their constraints which leads me to >> believe that the system is moving too far from where it was energy >> minimized. Errors such as: >> >> Step 188, time 0.376 (ps) >> LINCS WARNING >> relative constraint deviation after LINCS: >> rms 0.000017, max 0.000636 (between atoms 9 and 68) >> bonds that rotated more than 30 degrees: >> atom 1 atom 2 angle previous, current, constraint length >> 9 68 31.2 0.1111 0.1110 0.1111 >> >> Step 188, time 0.376 (ps) LINCS WARNING >> relative constraint deviation after LINCS: >> rms 0.000015, max 0.000531 (between atoms 9 and 68) >> bonds that rotated more than 30 degrees: >> atom 1 atom 2 angle previous, current, constraint length >> 9 68 31.0 0.1111 0.1110 0.1111 >> >> >> **Please, if anybody can help, I would greatly appreciate it. Thanks. >> -- >> Best regards, >> >> Fabian F. Casteblanco >> Rutgers University -- >> Chemical Engineering >> C: +908 917 0723 >> E: fabian.castebla...@gmail.com >> > > > > -- > Best regards, > > Fabian F. Casteblanco > Rutgers University -- > Chemical Engineering PhD Student > C: +908 917 0723 > E: fabian.castebla...@gmail.com > -- Best regards, Fabian F. Casteblanco Rutgers University -- Chemical Engineering PhD Student C: +908 917 0723 E: fabian.castebla...@gmail.com -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists
