Re: [gmx-users] Shift functions
On 10 February 2012 09:41, Mark Abraham wrote: > On 11/02/2012 1:19 AM, Elisabeth wrote: > > > Hello all, >> >> Does the shift function use group based truncation? >> >> >> See the discussion of charge groups in manual section 3.4.2. >> > > Thanks Mark. > > -1- First of all if I am right charge groups in gromacs language in > identical to "group based truncations"? > > > Using charge groups as the indivisible entity upon which neighbour list > construction is based is using "group based truncations". The usual > alternative is using atoms as the, well, *atomic* unit. The former can be > equivalent to the latter if there's one atom per charge group. > > > > > Manual 342: "This reduces the cut-off effects from the charge-charge > level to the dipole-dipole level, which decay much faster" > > 2- I am not able to realize why we go from charge-charge the dipole-dipole > changes? > > > Charge groups are constructed to have neutral charge (or integer charge > where necessary). To first order, the difference between any such group > being in the neighbour list of another such group or not (according to the > cut-off radius) is equivalent to a point dipole being in the cut-off sphere > or not. Charge groups with arbitrary charge (or partially-charged atoms, > when using atom-based truncation) do not have this quality, and the > distance at which a charge-charge interaction is significant is much larger > than that of a dipole-dipole. > > > > > >In the manual I see: by using shifted forces there is no need for >> charge groups (=group based?!) in the neighbor list? >> >> Can anyone shed some light on calculation of shifted forces? >> >> >> What's not clear from the above and 4.1.5? >> > > 3- I understand that use of shift makes the potentials have continuous > derivatives at cutoffs but that how this makes use of charge groups > unnecessary, I dont see! > > > Remember that the neighbour list is constructed to permit the computation > of a finite number of interactions with the central atom/group. You want to > stop computing them when they're close enough to zero that you don't care. > If they actually go to zero, then you don't care. If they decay as 1/r > (charge-charge) then at typical r_c values you should care. If they decay > as 1/r^2 (dipole-dipole, IIRC) then at typical r_c values things are OK. > > If the value of the force is non-zero at the cut-off, then there is an > interaction at that distance and not one just past that distance. This > generates artefacts that are serious for non-zero charges at the kinds of > cut-off distances for which force fields are parametrized, but much less > serious if computed over neutral charge groups. > > If the value of the force is zero at the cut-off (i.e. shift potential), > then no atom or charge group has any interaction with the central > group/atom at that distance, > > so you don't need to care about whether the truncation is based on atoms > or groups. You do have to care about the effect of the modified Coulomb > potential, however. > > Hello Mark, > I read over your answer several times. I am still unclear about " modified Coulomb potential". In the manual modified Coulomb potential refers to shift/switch functions, as I realized. so when the force is zero at r_c and it doesnt matter whether truncation is based on atoms or groups, why effect of modified coulomb potential is important? > > > > > -- gmx-users mailing listgmx-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
[gmx-users] Re: improper dihedral angle in charmm and opls aa (Mark Abraham)
Dear Mark and Gromacs Users, Can you be more specific in explanation about improper dihedral of charmm in gromacs? For opls aa, it is very clear that every item of improper dihedral angle is described once on the *rtp file. I am quite confused about the one in the charmm. Ihe same angle is sometimes described twice despite of the difference in the atoms' sequence. Suposed for an unkown molecule, how to assign them on rtp file? Can you give some introduction or show somewhere that has the document? Gromacs menu does not document about this. Thanks for advance! Tom > > Message: 1 > Date: Sat, 11 Feb 2012 11:15:04 +1100 > From: Mark Abraham > Subject: Re: [gmx-users] improper dihedral angle in charmm and opls aa > To: Discussion list for GROMACS users > Message-ID: <4f35b308.3080...@anu.edu.au> > Content-Type: text/plain; charset="iso-8859-1" > > On 11/02/2012 9:54 AM, Tom wrote: > > Dear Gromacs Users > > I am confused about definition of improper dihedral angle in charmm27, > > which is compared to oplsaa. > > Why charmm ff in gromacs give *double* items for the same dihedral angle. > > e.g. for charmm27 ASN > > CG ND2 CB OD1 > > CG CB ND2 OD1 > > ND2 CG HD21HD22 > > ND2 CG HD22HD21 > > These are not duplicates. Atom ordering is significant. These *improper* > dihedral angles are enforcing planarity of the amide moiety. This is > done by influencing dihedral angles along intra-atom vectors where there > is no bond. OPLS/AA is working differently somehow. > > Mark > > > in opls aa for ASN > > CGCBCA C dih_ASN_chi1_C_C_C_CO > > CACBCG ND2 dih_ASN_chi2_C_C_CO_N > > Thanks for advance! > > Tom > > PS: > > the detail is as follows > > > > *in charmm27.ff/aminoacids.rtp* > > [ ASN ] > > [ atoms ] > > N NH1 -0.47 0 > > HN H 0.311 > > CA CT1 0.072 > > HA HB 0.093 > > CB CT2 -0.18 4 > > HB1 HA 0.095 > > HB2 HA 0.096 > > CG CC 0.557 > > OD1 O -0.55 8 > > ND2 NH2 -0.62 9 > > HD21H 0.3210 > > HD22H 0.3011 > > C C 0.5112 > > O O -0.51 13 > > [ bonds ] > > CB CA > > CG CB > > ND2 CG > > N HN > > N CA > > C CA > > C +N > > CA HA > > CB HB1 > > CB HB2 > > ND2 HD21 > > ND2 HD22 > > C O > > CG OD1 > > [ impropers ] > > N -C CA HN > > C CA +N O > > CG ND2 CB OD1 > > CG CB ND2 OD1 > > ND2 CG HD21HD22 > > ND2 CG HD22HD21 > > [ cmap ] > > -C N CA C +N > > --- > > in*oplsaa.ff/aminoacids.rtp* > > [ ASN ] > > [ atoms ] > > Nopls_238 -0.500 0 > > Hopls_2410.300 0 > > CAopls_224B 0.140 1 > > HAopls_1400.060 1 > > CBopls_136 -0.120 2 > >HB1opls_1400.060 2 > >HB2opls_1400.060 2 > > CGopls_2350.500 3 > >OD1opls_236 -0.500 3 > >ND2opls_237 -0.760 4 > > HD21opls_2400.380 4 > > HD22opls_2400.380 4 > > Copls_2350.500 5 > > Oopls_236 -0.500 5 > > [ bonds ] > > N H > > NCA > > CAHA > > CACB > > CA C > > CB HB1 > > CB HB2 > > CBCG > > CG OD1 > > CG ND2 > >ND2 HD21 > >ND2 HD22 > > C O > > -C N > > [ dihedrals ] ; override some with residue-specific ones > > NCACBCG dih_ASN_chi1_N_C_C_C > > CGCBCA C dih_ASN_chi1_C_C_C_CO > > CACBCG ND2 dih_ASN_chi2_C_C_CO_N > > > > > > -- next part -- > An HTML attachment was scrubbed... > URL: > http://lists.gromacs.o
[gmx-users] Umbrella Sampling
Dear Gmx Users, I run a simulation of a protein and 10 ligands. They all stacked on the protein surface. I extracted the coordinates of the somplex and I am doing Umbrella Sampling - I am trying to pull one of the ligand from my protein. My questions: Would you suggest restarining positions of the protein (and 9 other ligands?) when pulling my ligand? Would you restrained positions of the protein when running simulations in each window? How do you adjust the pulling constant force? Is there any rule or you just change it and observe? Thank you, Steven -- gmx-users mailing listgmx-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
[gmx-users] Re: improper dihedral angle in charmm and opls aa (Mark Abraham)
gt; NCA > CAHA > CACB > CA C > CB HB1 > CB HB2 > CBCG > CG OD1 > CG ND2 >ND2 HD21 >ND2 HD22 > C O > -C N > [ dihedrals ] ; override some with residue-specific ones > NCA CB CG dih_ASN_chi1_N_C_C_C > CGCBCA C dih_ASN_chi1_C_C_C_CO > CACBCG ND2 dih_ASN_chi2_C_C_CO_N > > -- next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20120211/a4d6d18e/attachment-0001.html -- gmx-users mailing listgmx-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
[gmx-users] co-solvent simulation
I am simulating a protein in glycerol solution in amber03 ff and followed "http://www.gromacs.org/Documentation/How-tos/Mixed_Solvents";. Since glycerol is not available in amber03.ff by default, I built it in the ffbonded.itp and aminoacids.rtp. For test purpose, I then made a itp for it and solvate it as a protein and changed .top file accordingly, everything seems fine when I grompp, but when I insert it as a co-solvent, it shows like that I never did claim any bond angles, dihedrals, even when I #include its .itp and change #mols in my new topology. I guess the problem is if I do not claim the co-solvent as a protein, ff will not go to ffbonded.itp to recognize the new interactions. Is there any other file for co-solvent interactions I need to change? Thanks, Yao -- gmx-users mailing listgmx-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
[gmx-users] co-solvent simulation
I am simulating a protein in glycerol solution in amber03 ff and followed "http://www.gromacs.org/Documentation/How-tos/Mixed_Solvents";. Since glycerol is not available in amber03.ff by default, I built it in the ffbonded.itp and aminoacids.rtp. For test purpose, I then made a itp for it and solvate it as a protein and changed .top file accordingly, everything seems fine when I grompp, but when I insert it as a co-solvent, it shows like that I never did claim any bond angles, dihedrals, even when I #include its .itp and change #mols in my new topology. I guess the problem is if I do not claim the co-solvent as a protein, ff will not go to ffbonded.itp to recognize the new interactions. Is there any other file for co-solvent interactions I need to change? Thanks, Yao-- gmx-users mailing listgmx-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
Re: [gmx-users] co-solvent simulation
On 12/02/2012 4:16 PM, Yao Yao wrote: I am simulating a protein in glycerol solution in amber03 ff and followed "http://www.gromacs.org/Documentation/How-tos/Mixed_Solvents";. Since glycerol is not available in amber03.ff by default, I built it in the ffbonded.itp You should not need to touch this file to model glycerol. There are no atom or interaction types that are materially different from those on peptide side chains. and aminoacids.rtp. For test purpose, I then made a itp for it and solvate it as a protein and changed .top file accordingly, everything seems fine when I grompp, but when I insert it as a co-solvent, it shows like that I never did claim any bond angles, dihedrals, even when I #include its .itp and change #mols in my new topology. You need to work out what is different in the two cases. The diff tool can be useful here. There is no fundamental difference in the .top construction for the two cases you are considering - only in construction of the initial coordinates. I guess the problem is if I do not claim the co-solvent as a protein, ff will not go to ffbonded.itp to recognize the new interactions. Is there any other file for co-solvent interactions I need to change? The ffbonded.itp file is #included regardless of what you name your moleculetypes. You may not be #including the correct one - but then again I think you should only have the standard one in the first place. Mark -- gmx-users mailing listgmx-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
Re: [gmx-users] co-solvent simulation
Hi Mark, Thanks for your reply. I have not figured out what the problem. BUt I am thinking if I have two proteins in my system, like simulating the protein-protein interaction, what I should call the second protein for [moleculetype] in my .top, still "protein"? Thanks, Yao From: Mark Abraham To: Discussion list for GROMACS users Sent: Saturday, February 11, 2012 9:39 PM Subject: Re: [gmx-users] co-solvent simulation On 12/02/2012 4:16 PM, Yao Yao wrote: I am simulating a protein in glycerol solution in amber03 ff and followed "http://www.gromacs.org/Documentation/How-tos/Mixed_Solvents";. >Since glycerol is not available in amber03.ff by default, I built it in the >ffbonded.itp You should not need to touch this file to model glycerol. There are no atom or interaction types that are materially different from those on peptide side chains. and aminoacids.rtp. >For test purpose, I then made a itp for it and solvate it as a protein and >changed .top file accordingly, everything seems fine when I grompp, >but when I insert it as a co-solvent, it shows like that I never did claim any >bond angles, dihedrals, even when I #include its .itp and change #mols in >my new topology. > You need to work out what is different in the two cases. The diff tool can be useful here. There is no fundamental difference in the .top construction for the two cases you are considering - only in construction of the initial coordinates. > >I guess the problem is if I do not claim the co-solvent as a protein, ff will >not go to ffbonded.itp to recognize the new interactions. >Is there any other file for co-solvent interactions I need to change? The ffbonded.itp file is #included regardless of what you name your moleculetypes. You may not be #including the correct one - but then again I think you should only have the standard one in the first place. Mark -- 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-- gmx-users mailing listgmx-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
[gmx-users] co-solvent simulation
Actually even I follow the ""http://www.gromacs.org/Documentation/How-tos/Mixed_Solvents"and try the built-in ureaas co-solvent, it has the same problem (solvate urea as protein can work, but does not work if you consider it as co-solvent). I do not know if anyone has met the same problem before. Thanks, Yao - Forwarded Message - From: Yao Yao To: Discussion list for GROMACS users Sent: Saturday, February 11, 2012 10:47 PM Subject: Re: [gmx-users] co-solvent simulation Hi Mark, Thanks for your reply. I have not figured out what the problem. BUt I am thinking if I have two proteins in my system, like simulating the protein-protein interaction, what I should call the second protein for [moleculetype] in my .top, still "protein"? Thanks, Yao From: Mark Abraham To: Discussion list for GROMACS users Sent: Saturday, February 11, 2012 9:39 PM Subject: Re: [gmx-users] co-solvent simulation On 12/02/2012 4:16 PM, Yao Yao wrote: I am simulating a protein in glycerol solution in amber03 ff and followed "http://www.gromacs.org/Documentation/How-tos/Mixed_Solvents";. >Since glycerol is not available in amber03.ff by default, I built it in the >ffbonded.itp You should not need to touch this file to model glycerol. There are no atom or interaction types that are materially different from those on peptide side chains. and aminoacids.rtp. >For test purpose, I then made a itp for it and solvate it as a protein and >changed .top file accordingly, everything seems fine when I grompp, >but when I insert it as a co-solvent, it shows like that I never did claim any >bond angles, dihedrals, even when I #include its .itp and change #mols in >my new topology. > You need to work out what is different in the two cases. The diff tool can be useful here. There is no fundamental difference in the .top construction for the two cases you are considering - only in construction of the initial coordinates. > >I guess the problem is if I do not claim the co-solvent as a protein, ff will >not go to ffbonded.itp to recognize the new interactions. >Is there any other file for co-solvent interactions I need to change? The ffbonded.itp file is #included regardless of what you name your moleculetypes. You may not be #including the correct one - but then again I think you should only have the standard one in the first place. Mark -- 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-- gmx-users mailing listgmx-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
Re: [gmx-users] co-solvent simulation
Please disregard my previous email. I made a minor mistake when I built the .top file. Thanks, Yao From: Yao Yao To: "gmx-users@gromacs.org" Sent: Saturday, February 11, 2012 11:06 PM Subject: [gmx-users] co-solvent simulation Actually even I follow the ""http://www.gromacs.org/Documentation/How-tos/Mixed_Solvents"and try the built-in ureaas co-solvent, it has the same problem (solvate urea as protein can work, but does not work if you consider it as co-solvent). I do not know if anyone has met the same problem before. Thanks, Yao - Forwarded Message - From: Yao Yao To: Discussion list for GROMACS users Sent: Saturday, February 11, 2012 10:47 PM Subject: Re: [gmx-users] co-solvent simulation Hi Mark, Thanks for your reply. I have not figured out what the problem. BUt I am thinking if I have two proteins in my system, like simulating the protein-protein interaction, what I should call the second protein for [moleculetype] in my .top, still "protein"? Thanks, Yao From: Mark Abraham To: Discussion list for GROMACS users Sent: Saturday, February 11, 2012 9:39 PM Subject: Re: [gmx-users] co-solvent simulation On 12/02/2012 4:16 PM, Yao Yao wrote: I am simulating a protein in glycerol solution in amber03 ff and followed "http://www.gromacs.org/Documentation/How-tos/Mixed_Solvents";. >Since glycerol is not available in amber03.ff by default, I built it in the >ffbonded.itp You should not need to touch this file to model glycerol. There are no atom or interaction types that are materially different from those on peptide side chains. and aminoacids.rtp. >For test purpose, I then made a itp for it and solvate it as a protein and >changed .top file accordingly, everything seems fine when I grompp, >but when I insert it as a co-solvent, it shows like that I never did claim any >bond angles, dihedrals, even when I #include its .itp and change #mols in >my new topology. > You need to work out what is different in the two cases. The diff tool can be useful here. There is no fundamental difference in the .top construction for the two cases you are considering - only in construction of the initial coordinates. > >I guess the problem is if I do not claim the co-solvent as a protein, ff will >not go to ffbonded.itp to recognize the new interactions. >Is there any other file for co-solvent interactions I need to change? The ffbonded.itp file is #included regardless of what you name your moleculetypes. You may not be #including the correct one - but then again I think you should only have the standard one in the first place. Mark -- 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 -- 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-- gmx-users mailing listgmx-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
