Re: [gmx-users] Basic Query
priyanka srivastava wrote: Dear Prof. Spoel, Many thanks for your reply. Since the fourier_n* values are associated with the grid sizing, will these values affect my results drastically? do you suggest resubmitting these runs? regards, Pri... check your md.log file to see what was used. you need roughly 0.1-0.2 nm gridspacing depending on the cutoff. -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Basic Query
Dear Prof. Spoel, Many thanks for your reply. Since the fourier_n* values are associated with the grid sizing, will these values affect my results drastically? do you suggest resubmitting these runs? regards, Pri... David van der Spoel <[EMAIL PROTECTED]> wrote: priyanka srivastava wrote: > Hie, > > Many thanks for your reply. > > Yes I have used semi-isotropic coupling. > > Another doubt is why only a value of 4.5e-5? > > I have used PME and have mentioned rcoulomb in the > .mdp file too, which as is pointed out by you, has no > meaning!! But does this mean that my mdp file is > wrong? Because if PME does not use rcoulomb it shud > simply ignore the value. > Actually I do not want to use twin range cutoff. So, I > have given rvdw = rlist. Is this alright? > Portion of my mdp file looks like this: > > ; Electrostatics > coulombtype = PME > fourier_nx = 6.4 > fourier_ny = 5.0 > fourier_nz = 8.1 these numbers should be integers > pme_order = 4 > rcoulomb= 1.5 > rvdw= 1.5 > > Also since I have not specified "vdwtype" in the mdp > file, so it automatically takes Cut-off. > > regards, > Pri... > > > --- Martin H�fling wrote: > >> Am Mittwoch, 20. Juni 2007 schrieb priyanka >> srivastava: >> >>> I am currently involved in doing a lipid-peptide >>> simulation under NPAT conditions. The way I have >>> applied NPAT condition is as follows: >>> >>> ref_p = 0 1 >>> compressibility = 0.0 4.5e-5 >> with semiisotropic? >> >>> Although while performing analysis it shows that >> the x >>> and y dimensions are constant but still I am not >> sure >>> about the way I have applied NPAT. Could somone >> please >>> tell me the basis behind it? >> If i am remembering correctly, this is what above >> values should do: >> >> first dimension is x-y second one is the z >> direction. Reference pressure is 1 >> for both (obviously makes sense) whereas >> compressibility set to 0 for x-y >> plane prevents box changes in x and y direction. So >> only z-direction remains >> for adjusting pressure. >> >>> Another thing is I have used vdwtype: cutoff. >>> But my intention is not to use the twin range >> cutoff >>> at all!! In my case rlist = rcoulomb = rvdw, i.e. >> all >>> three are same!! Is this alright? (the coulombtype >>> = PME) >> Sorry, didn't get that part of your question. Can >> you post relevant parts of >> your mdp and specify it further? Chapter 7 says that >> parameters for PME are >> fourierspacing and pme_order, rcoulomb should not be >> used then. >> >> Cheers >> Martin >> ___ >> gmx-users mailing listgmx-users@gromacs.org >> http://www.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 >> [EMAIL PROTECTED] >> Can't post? Read >> http://www.gromacs.org/mailing_lists/users.php >> > > > > > > Pinpoint customers who are looking for what you sell. > http://searchmarketing.yahoo.com/ > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.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 [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php - Get the free Yahoo! toolbar and rest assured with the added security of spyware protection. ___ gmx-users mailing listgmx-users@gromacs.org http://www.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
Re: [gmx-users] Basic Query
Am Mittwoch, 20. Juni 2007 schrieb Mark Abraham: > As you'd see by reading sections 4.9 and 7.3.9 of the manual, Martin's > statement isn't right. The grid dimensions are controlled by the two > parameters he mentioned, but there are plenty of other parameters that > influence PME. Oh, I didn't checked 4.9. Then of course rlist makes sense too for coulomb interactions with PME. > Set it specifically, so that you don't have to remember what the default > is in a year's time. ... and look in your own mdp file before making statements :-) Best Martin ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Basic Query
priyanka srivastava wrote: Hie, Many thanks for your reply. Yes I have used semi-isotropic coupling. Another doubt is why only a value of 4.5e-5? I have used PME and have mentioned rcoulomb in the .mdp file too, which as is pointed out by you, has no meaning!! But does this mean that my mdp file is wrong? Because if PME does not use rcoulomb it shud simply ignore the value. Actually I do not want to use twin range cutoff. So, I have given rvdw = rlist. Is this alright? Portion of my mdp file looks like this: ; Electrostatics coulombtype = PME fourier_nx = 6.4 fourier_ny = 5.0 fourier_nz = 8.1 these numbers should be integers pme_order = 4 rcoulomb= 1.5 rvdw= 1.5 Also since I have not specified "vdwtype" in the mdp file, so it automatically takes Cut-off. regards, Pri... --- Martin Höfling <[EMAIL PROTECTED]> wrote: Am Mittwoch, 20. Juni 2007 schrieb priyanka srivastava: I am currently involved in doing a lipid-peptide simulation under NPAT conditions. The way I have applied NPAT condition is as follows: ref_p = 0 1 compressibility = 0.0 4.5e-5 with semiisotropic? Although while performing analysis it shows that the x and y dimensions are constant but still I am not sure about the way I have applied NPAT. Could somone please tell me the basis behind it? If i am remembering correctly, this is what above values should do: first dimension is x-y second one is the z direction. Reference pressure is 1 for both (obviously makes sense) whereas compressibility set to 0 for x-y plane prevents box changes in x and y direction. So only z-direction remains for adjusting pressure. Another thing is I have used vdwtype: cutoff. But my intention is not to use the twin range cutoff at all!! In my case rlist = rcoulomb = rvdw, i.e. all three are same!! Is this alright? (the coulombtype = PME) Sorry, didn't get that part of your question. Can you post relevant parts of your mdp and specify it further? Chapter 7 says that parameters for PME are fourierspacing and pme_order, rcoulomb should not be used then. Cheers Martin ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php Pinpoint customers who are looking for what you sell. http://searchmarketing.yahoo.com/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Basic Query
priyanka srivastava wrote: I have used PME and have mentioned rcoulomb in the .mdp file too, which as is pointed out by you, has no meaning!! But does this mean that my mdp file is wrong? Because if PME does not use rcoulomb it shud simply ignore the value. As you'd see by reading sections 4.9 and 7.3.9 of the manual, Martin's statement isn't right. The grid dimensions are controlled by the two parameters he mentioned, but there are plenty of other parameters that influence PME. You're right, in that if mdp file parameters will be ignored then the value you use isn't relevant. Actually I do not want to use twin range cutoff. So, I have given rvdw = rlist. Is this alright? Yes, see section 4.6.3. This is only relevant for vdw since coulombtype = PME Portion of my mdp file looks like this: ; Electrostatics coulombtype = PME fourier_nx = 6.4 fourier_ny = 5.0 fourier_nz = 8.1 pme_order = 4 rcoulomb= 1.5 rvdw= 1.5 Assuming you got these values from somewhere sensible and that they're consistent with the force field you're using, then this will give you some numbers that have at least as good a chance of corresponding to reality as anything :-) Also since I have not specified "vdwtype" in the mdp file, so it automatically takes Cut-off. Set it specifically, so that you don't have to remember what the default is in a year's time. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Basic Query
Hie, Many thanks for your reply. Yes I have used semi-isotropic coupling. Another doubt is why only a value of 4.5e-5? I have used PME and have mentioned rcoulomb in the .mdp file too, which as is pointed out by you, has no meaning!! But does this mean that my mdp file is wrong? Because if PME does not use rcoulomb it shud simply ignore the value. Actually I do not want to use twin range cutoff. So, I have given rvdw = rlist. Is this alright? Portion of my mdp file looks like this: ; Electrostatics coulombtype = PME fourier_nx = 6.4 fourier_ny = 5.0 fourier_nz = 8.1 pme_order = 4 rcoulomb= 1.5 rvdw= 1.5 Also since I have not specified "vdwtype" in the mdp file, so it automatically takes Cut-off. regards, Pri... --- Martin Höfling <[EMAIL PROTECTED]> wrote: > Am Mittwoch, 20. Juni 2007 schrieb priyanka > srivastava: > > > I am currently involved in doing a lipid-peptide > > simulation under NPAT conditions. The way I have > > applied NPAT condition is as follows: > > > > ref_p = 0 1 > > compressibility = 0.0 4.5e-5 > > with semiisotropic? > > > Although while performing analysis it shows that > the x > > and y dimensions are constant but still I am not > sure > > about the way I have applied NPAT. Could somone > please > > tell me the basis behind it? > > If i am remembering correctly, this is what above > values should do: > > first dimension is x-y second one is the z > direction. Reference pressure is 1 > for both (obviously makes sense) whereas > compressibility set to 0 for x-y > plane prevents box changes in x and y direction. So > only z-direction remains > for adjusting pressure. > > > Another thing is I have used vdwtype: cutoff. > > But my intention is not to use the twin range > cutoff > > at all!! In my case rlist = rcoulomb = rvdw, i.e. > all > > three are same!! Is this alright? (the coulombtype > > = PME) > > Sorry, didn't get that part of your question. Can > you post relevant parts of > your mdp and specify it further? Chapter 7 says that > parameters for PME are > fourierspacing and pme_order, rcoulomb should not be > used then. > > Cheers > Martin > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.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 > [EMAIL PROTECTED] > Can't post? Read > http://www.gromacs.org/mailing_lists/users.php > Pinpoint customers who are looking for what you sell. http://searchmarketing.yahoo.com/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Basic Query
Am Mittwoch, 20. Juni 2007 schrieb priyanka srivastava: > I am currently involved in doing a lipid-peptide > simulation under NPAT conditions. The way I have > applied NPAT condition is as follows: > > ref_p = 0 1 > compressibility = 0.0 4.5e-5 with semiisotropic? > Although while performing analysis it shows that the x > and y dimensions are constant but still I am not sure > about the way I have applied NPAT. Could somone please > tell me the basis behind it? If i am remembering correctly, this is what above values should do: first dimension is x-y second one is the z direction. Reference pressure is 1 for both (obviously makes sense) whereas compressibility set to 0 for x-y plane prevents box changes in x and y direction. So only z-direction remains for adjusting pressure. > Another thing is I have used vdwtype: cutoff. > But my intention is not to use the twin range cutoff > at all!! In my case rlist = rcoulomb = rvdw, i.e. all > three are same!! Is this alright? (the coulombtype > = PME) Sorry, didn't get that part of your question. Can you post relevant parts of your mdp and specify it further? Chapter 7 says that parameters for PME are fourierspacing and pme_order, rcoulomb should not be used then. Cheers Martin ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
