[gmx-users] Re: amber parameters in gromacs
Hold on, you said *amber*, nevertheless you top has definitions for GROMOS**. Either you are mixing force fields here (which *bad*) or worse, your not using Amber FF, which is *really bad*. I would be helpful if you give the commands you're using for pdb2gmx and grompp. Besides, are you aware of ffamber and acpype? Since you said you have the parameters for glycerol you may not need to build the topology anew, but I do recommend looking at acpype.googlecode.com to know more about simulations involving amber ff and gromacs, besides links to important resources like ffamber. Cheers, Alan On Thu, Jul 1, 2010 at 09:13, wrote: > Dear gromacs-users, > > I've been simulating a box of liquid glycerol. The parameter's I have used > were taken from an article, whose authors achieved good agreement between > their simulation and experiments. These authors used an amber force field > and the software ORAC. > > I used exactly the same parameters as them for my topology and very similar > settings in my mdp file. However I did not get the same results as them. Do > you know why I get these different results? I am in doubt weather the top of > my topology is correct, so I pasted it here: > > #define _FF_GROMOS96 > #define _FF_GROMOS53A6 > > [ defaults ] > ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ > 12 yes 0.5 0.8333 > > [ atomtypes ] > ;name at.num mass charge ptype sigma epsilon >OA 8 0.000 0.000 A 0.34420.879228 >C 6 0.000 0.000 A 0.38160.45803592 >H 1 0.000 0.000 A 0 0 >HC 1 0.000 0.000 A 0.27740.06573276 > > > [ moleculetype ] > > Glycerol 3 > > [ atoms ] > ; nr type resnr resid atom cgnr charge > 1 OA 1 GLCR OAA1 -0.58515.9994 > 2 H 1 GLCR HAA1 0.3961.008 > 3 C 1 GLCR CAD1 0.18212.011 >. > > I think, that by specifying comb-rule = 2 giving sigma and epsilon is > correct instead of c6 and c12. The 0.5 for fudgeLJ and the 0.8333 for > fudgeQQ are supposed to lower the 1-4 interaction. > > Regards, > > Rolf > -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. >>http://www.bio.cam.ac.uk/~awd28<< -- gmx-users mailing listgmx-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
[gmx-users] Re: amber parameters in gromacs
Hi, I used the GROMOS FF but changed the parameters (sigma, epsilon, charges, 1-4 interaction, combination rule for LJ, bond length strength, dihedrals, angles) so that they are equal to the parameters used by the other authors with their AMBER FF. The equations uses to calculate the energy are the same, that is why I expected to get the same results. ...so I guess this assumption is not true. Why is it not possible to use these parameters? Is there a way to get a topology of glycerol working with gromacs instead of writing it oneself? I've already tried the Prodrg Server but I didn't get proper results with this topology, either. Regards, Rolf On 07/01/10, Alan wrote: > Hold on, you said *amber*, nevertheless you top has definitions for GROMOS**. > Either you are mixing force fields here (which *bad*) or worse, your not > using Amber FF, which is *really bad*. > > > I would be helpful if you give the commands you're using for pdb2gmx and > grompp. Besides, are you aware of ffamber and acpype? Since you said you have > the parameters for glycerol you may not need to build the topology anew, but > I do recommend looking at acpype.googlecode.com(http://acpype.googlecode.com) > to know more about simulations involving amber ff and gromacs, besides links > to important resources like ffamber. > > > > > Cheers, > > > Alan > > > > > On Thu, Jul 1, 2010 at 09:13, > wrote: > > > > > > > Dear gromacs-users, > > > > > > > > I've been simulating a box of liquid glycerol. The parameter's I have used > > were taken from an article, whose authors achieved good agreement between > > their simulation and experiments. These authors used an amber force field > > and the software ORAC. > > > > > > > > > > > > I used exactly the same parameters as them for my topology and very similar > > settings in my mdp file. However I did not get the same results as them. Do > > you know why I get these different results? I am in doubt weather the top > > of my topology is correct, so I pasted it here: > > > > > > > > > > > > #define _FF_GROMOS96 > > > > #define _FF_GROMOS53A6 > > > > > > > > [ defaults ] > > > > ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ > > > > 1 2 yes 0.5 0.8333 > > > > > > > > [ atomtypes ] > > > > ;name at.num mass charge ptype sigma epsilon > > > > OA 8 0.000 0.000 A 0.3442 0.879228 > > > > C 6 0.000 0.000 A 0.3816 0.45803592 > > > > H 1 0.000 0.000 A 0 0 > > > > HC 1 0.000 0.000 A 0.2774 0.06573276 > > > > > > > > > > > > [ moleculetype ] > > > > > > > > Glycerol 3 > > > > > > > > [ atoms ] > > > > ; nr type resnr resid atom cgnr charge > > > > 1 OA 1 GLCR OAA 1 -0.585 15.9994 > > > > 2 H 1 GLCR HAA 1 0.396 1.008 > > > > 3 C 1 GLCR CAD 1 0.182 12.011 > > > > . > > > > > > > > I think, that by specifying comb-rule = 2 giving sigma and epsilon is > > correct instead of c6 and c12. The 0.5 for fudgeLJ and the 0.8333 for > > fudgeQQ are supposed to lower the 1-4 interaction. > > > > > > > > Regards, > > > > > > > > Rolf > > > > > > -- > Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate > Department of Biochemistry, University of Cambridge. > 80 Tennis Court Road, Cambridge CB2 1GA, UK. > > > >>http://www.bio.cam.ac.uk/~awd28<< -- gmx-users mailing listgmx-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
[gmx-users] Re: amber parameters in gromacs
Hi Rolf, On Thu, Jul 1, 2010 at 10:23, wrote: > I used the GROMOS FF but changed the parameters (sigma, epsilon, charges, > 1-4 interaction, combination rule for LJ, bond length strength, dihedrals, > angles) so that they are equal to the parameters used by the other authors > with their AMBER FF. The equations uses to calculate the energy are the > same, that is why I expected to get the same results. ...so I guess this > assumption is not true. Why is it not possible to use these parameters? > I understand that you're trying to simulate *only* glycerol and nothing else. In principle your idea does hold water, but in the end it's full of holes. GROMOS FF is conceived as an united-atom ff even if you have all protons explicit. The biggest difference among others I see is the way how dihedrals will be calculated. BTW, where's the reference to the article you mentioned? Do you want to rule out these potentials problems? Re-read the first email I sent and do check the links I provided. From there you can start to know how to use ffamber or, if you have your parameters in amber format (do you know how to use tleap from AmberTools to generate a prmtop and inpcrd files?), to use acpype (or amb2gmx) to convert them to gromacs format straightaway. > Is there a way to get a topology of glycerol working with gromacs instead > of writing it oneself? I've already tried the Prodrg Server but I didn't get > proper results with this topology, either. > The basic answer is "yes" and my attempt to to answer that is above. Cheers, Alan -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. >>http://www.bio.cam.ac.uk/~awd28<< -- gmx-users mailing listgmx-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
Re: [gmx-users] Re: amber parameters in gromacs
On 2010-07-01 11.19, Rolf Erwin Isele-Holder wrote: Hi, I used the GROMOS FF but changed the parameters (sigma, epsilon, charges, 1-4 interaction, combination rule for LJ, bond length strength, dihedrals, angles) so that they are equal to the parameters used by the other authors with their AMBER FF. The equations uses to calculate the energy are the same, that is why I expected to get the same results. ...so I guess this assumption is not true. Why is it not possible to use these parameters? Is there a way to get a topology of glycerol working with gromacs instead of writing it oneself? I've already tried the Prodrg Server but I didn't get proper results with this topology, either. in order to debug these things you need to compare energies at step zero, preferably for one molecule first. IIRC amber does not use the factor 1/2 in harmonic potentials, so you would have to multiply the force constant by two. Regards, Rolf On 07/01/10, Alan wrote: Hold on, you said *amber*, nevertheless you top has definitions for GROMOS**. Either you are mixing force fields here (which *bad*) or worse, your not using Amber FF, which is *really bad*. I would be helpful if you give the commands you're using for pdb2gmx and grompp. Besides, are you aware of ffamber and acpype? Since you said you have the parameters for glycerol you may not need to build the topology anew, but I do recommend looking at acpype.googlecode.com(http://acpype.googlecode.com) to know more about simulations involving amber ff and gromacs, besides links to important resources like ffamber. Cheers, Alan On Thu, Jul 1, 2010 at 09:13,> wrote: Dear gromacs-users, I've been simulating a box of liquid glycerol. The parameter's I have used were taken from an article, whose authors achieved good agreement between their simulation and experiments. These authors used an amber force field and the software ORAC. I used exactly the same parameters as them for my topology and very similar settings in my mdp file. However I did not get the same results as them. Do you know why I get these different results? I am in doubt weather the top of my topology is correct, so I pasted it here: #define _FF_GROMOS96 #define _FF_GROMOS53A6 [ defaults ] ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ 12 yes 0.5 0.8333 [ atomtypes ] ;name at.num mass charge ptype sigma epsilon OA 8 0.000 0.000 A 0.34420.879228 C 6 0.000 0.000 A 0.38160.45803592 H 1 0.000 0.000 A 0 0 HC 1 0.000 0.000 A 0.27740.06573276 [ moleculetype ] Glycerol 3 [ atoms ] ; nr type resnr resid atom cgnr charge 1 OA 1 GLCR OAA1 -0.58515.9994 2 H 1 GLCR HAA1 0.3961.008 3 C 1 GLCR CAD1 0.18212.011 . I think, that by specifying comb-rule = 2 giving sigma and epsilon is correct instead of c6 and c12. The 0.5 for fudgeLJ and the 0.8333 for fudgeQQ are supposed to lower the 1-4 interaction. Regards, Rolf -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. http://www.bio.cam.ac.uk/~awd28<< -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-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
