Dear all, I am trying to use g_velacc to calculate diffusion coefficient for a single polymer chain. As I follow the Gromacs tutorial and use the command (version 4.5.1)
g_velacc -acflen 1001 -nonormalize -mol -n atoms.ndx -s topol.tpr the ACF is always zero. However, if I remove -mol option, the data shows up. It looks like -mol is a default option for the calculation so I don't know if it is still necessary to add it, or is it just a bug in the program? Thank you! Shirley On May 22, 2013, at 10:31 AM, <gmx-users-requ...@gromacs.org> wrote: > Send gmx-users mailing list submissions to > gmx-users@gromacs.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://lists.gromacs.org/mailman/listinfo/gmx-users > or, via email, send a message with subject or body 'help' to > gmx-users-requ...@gromacs.org > > You can reach the person managing the list at > gmx-users-ow...@gromacs.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of gmx-users digest..." > > > Today's Topics: > > 1. Free energy of solvation's .mdp of peptide (maggin) > 2. Re: MSD and frequency of writing trajectories (Erik Marklund) > 3. Re: MSD and frequency of writing trajectories (Mark Abraham) > 4. Re: error in running g_dist (Mark Abraham) > 5. C6 & C12 parameters for non-bonded interactions using tables > (Andrish Reddy) > 6. Re: error in running g_dist (Andrish Reddy) > 7. Re: C6 & C12 parameters for non-bonded interactions using > tables (Mark Abraham) > 8. COM coordinate fix (l....@utwente.nl) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 22 May 2013 04:14:31 -0700 (PDT) > From: maggin <maggin.c...@gmail.com> > Subject: [gmx-users] Free energy of solvation's .mdp of peptide > To: gmx-users@gromacs.org > Message-ID: <1369221271481-5008445.p...@n6.nabble.com> > Content-Type: text/plain; charset=us-ascii > > Hi, if I want to calculate the free energy of solvation of peptide, because > both van der Waals and Coulombic interactions are important for peptide > > so I set couple-lambda0 = none > couple-lambda1 = vdw-q > > is it right? > > or it's better to choose wo-stage approach to do this work: > > van der Waals coupling: > > sc-alpha = 0.5 ; use soft-core for LJ (de)coupling > sc-sigma = 0.3 > sc-power = 1 > couple-moltype = peptide > couple-intramol = no > couple-lambda0 = none ; non-interacting dummy in state A > couple-lambda1 = vdw ; only vdW terms on in state B > Coulombic coupling: > > sc-alpha = 0 ; soft-core during (dis)charging can be > unstable! > sc-sigma = 0 > couple-moltype = peptide > couple-intramol = no > couple-lambda0 = vdw ; only vdW terms in state A (the previous > state B is now A) > couple-lambda1 = vdw-q ; all nonbonded interactions are on in > state B > > Thank you very much! > > maggin > > > > > > > -- > View this message in context: > http://gromacs.5086.x6.nabble.com/Free-energy-of-solvation-s-mdp-of-peptide-tp5008445.html > Sent from the GROMACS Users Forum mailing list archive at Nabble.com. > > > ------------------------------ > > Message: 2 > Date: Wed, 22 May 2013 13:17:41 +0200 > From: Erik Marklund <er...@xray.bmc.uu.se> > Subject: Re: [gmx-users] MSD and frequency of writing trajectories > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <1efe1d47-497a-44fc-99b2-a8210d2c0...@xray.bmc.uu.se> > Content-Type: text/plain; charset=us-ascii > > Hi, > > For particles that diffuse more than half a box length between frames will > appear as if they haven't moved much, assuming you have periodic boundary > conditions. > > Erik > > On 22 May 2013, at 11:41, Anna Akinshina <anna.akinsh...@manchester.ac.uk> > wrote: > >> Dear Gromacs Users, >> >> I have a question interpreting obtained msd data. >> I need to calculate diffusion coefficient for a single argon atom in a box >> of water (500 molecules). >> During the calculations (50ns) I write both trr and xtc trajectories, but to >> save space I write trr for whole system very seldom (every 50000 steps = 100 >> ps) >> but in xtc I have argon only (no water) and write more often (every 1000 >> steps = 2 ps). >> >> When I analysed the results using g_msd I was surprised that the msd curves >> obtained from trr and xtc trajectories differ a lot, what affect the >> resulting diffusion coefficients. >> >> If I save trr more often, like every 10000 steps (20ps) the results from >> both files coincide. >> >> Does the msd results depend on how often you write trajectories? >> If yes, what frequency for writing the trajectories for future calculation >> of the diffusion coefficient would be reasonable and how long should be the >> calculations? >> >> Thanks you >> Anna >> ----------------------- >> Dr Anna Akinshina >> School of Chemical Engineering & Analytical Science >> The University of Manchester, UK >> >> >> -- >> 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 > > > > ------------------------------ > > Message: 3 > Date: Wed, 22 May 2013 13:19:50 +0200 > From: Mark Abraham <mark.j.abra...@gmail.com> > Subject: Re: [gmx-users] MSD and frequency of writing trajectories > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: > <camnumasm86_nmlfcxhezkr2tmmdaifwprbnogvhfow+nxdv...@mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > Sure. What's the MSD of a pendulum if you only sample at a rate equal to > the period? How often you want to sample depends on the time scale of what > you want to observe. That might be up to you to measure :-) > > Mark > > > On Wed, May 22, 2013 at 11:41 AM, Anna Akinshina < > anna.akinsh...@manchester.ac.uk> wrote: > >> Dear Gromacs Users, >> >> I have a question interpreting obtained msd data. >> I need to calculate diffusion coefficient for a single argon atom in a box >> of water (500 molecules). >> During the calculations (50ns) I write both trr and xtc trajectories, but >> to save space I write trr for whole system very seldom (every 50000 steps = >> 100 ps) >> but in xtc I have argon only (no water) and write more often (every 1000 >> steps = 2 ps). >> >> When I analysed the results using g_msd I was surprised that the msd >> curves obtained from trr and xtc trajectories differ a lot, what affect >> the resulting diffusion coefficients. >> >> If I save trr more often, like every 10000 steps (20ps) the results from >> both files coincide. >> >> Does the msd results depend on how often you write trajectories? >> If yes, what frequency for writing the trajectories for future calculation >> of the diffusion coefficient would be reasonable and how long should be the >> calculations? >> >> Thanks you >> Anna >> ----------------------- >> Dr Anna Akinshina >> School of Chemical Engineering & Analytical Science >> The University of Manchester, UK >> >> >> -- >> 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 >> > > > ------------------------------ > > Message: 4 > Date: Wed, 22 May 2013 13:21:43 +0200 > From: Mark Abraham <mark.j.abra...@gmail.com> > Subject: Re: [gmx-users] error in running g_dist > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: > <camnumaq_vmbs1vyhhawxexq_9t6pncvumxa7wwf-whhpj6-...@mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > Use gmxcheck to find out what's in the files. Think about how you used > xtcgroups. Consider using tpbconv to make a matching subset from your .tpr. > > Mark > > > On Wed, May 22, 2013 at 11:53 AM, Arunima Shilpi > <writetoas...@gmail.com>wrote: > >> Respected sir >> >> I want to calculate the distance between protein and ligand after I have >> run the production step. I used the following command.. >> >> g_dist -s md_0_1.tpr -f md_0_1.xtc -o dist.xvg -n index.ndx >> >> Groups I selected was >> Group 1 (protein) >> Group 13 (ligand) >> >> It says the following error >> >> Molecule in topology has atom numbers below and above natoms (11793). >> You are probably trying to use a trajectory which does not match the first >> 11793 atoms of the run input file. >> >> how to debug the error... >> >> -- >> >> Thanking You with Regards. >> >> Arunima Shilpi >> >> Ph. D Research Scholar(Cancer & Epigenetics) >> Department of Life Science >> National Institute of Technology >> Rourkela >> Odisha >> -- >> 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 >> > > > ------------------------------ > > Message: 5 > Date: Wed, 22 May 2013 07:09:36 -0700 (PDT) > From: Andrish Reddy <are...@csir.co.za> > Subject: [gmx-users] C6 & C12 parameters for non-bonded interactions > using tables > To: gmx-users@gromacs.org > Message-ID: <1369231776546-5008449.p...@n6.nabble.com> > Content-Type: text/plain; charset=us-ascii > > Greetings, > > I am trying to use tabulated potentials for the VdW interactions between > TIP5P water molecules. > I have tested my topology file to make sure that it gives reasonable results > with the standard table6-12.xvg in the /top folder and C6=4*eps*sig^6 , > C12=4*eps*sig^12. I am able to match the energies with an identical run not > using look-up tables. The problem comes when I want to include the C6 & C12 > parameters within the table. This is needed for dealing with more complex > multi-parameter potential functions. > > I tried testing this with the standard Lennard-Jones potential. Setting > g(r)=-(4*eps*sig^6)/r^6 and h(r)=(4*eps*sig^12)/r^12. I then construct my > table according to [r,f(r),-f'(r),g(r),-g'(r),h(r),-h'(r)] > > I set vdw-type = user in my mdp file and modified my topology so that: > [ defaults ] > ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ > 1 1 yes 0.5 0.8333 > > [ atomtypes ] > ; name at.num mass charge ptype C6 C12 > OW_tip5p 8 16.00 0.0000 A 1.00000e+00 1.00000e+00 > > Since C6 & C12 = 1, this run should be identical to using the table6-12.xvg > and C6=4*eps*sig^6 , C12=4*eps*sig^12 > The run proceeds fine with no warnings or errors, but the LJ and Potential > energies are an order of magnitude higher than when using the standard > table. I don't understand why I am not able to reproduce the results by this > method? > > Thanks, > Andrish > > > > > -- > View this message in context: > http://gromacs.5086.x6.nabble.com/C6-C12-parameters-for-non-bonded-interactions-using-tables-tp5008449.html > Sent from the GROMACS Users Forum mailing list archive at Nabble.com. > > > ------------------------------ > > Message: 6 > Date: Wed, 22 May 2013 07:20:36 -0700 (PDT) > From: Andrish Reddy <are...@csir.co.za> > Subject: [gmx-users] Re: error in running g_dist > To: gmx-users@gromacs.org > Message-ID: <1369232436002-5008450.p...@n6.nabble.com> > Content-Type: text/plain; charset=us-ascii > > Arunima Shilpi-2 wrote >> Respected sir >> >> I want to calculate the distance between protein and ligand after I have >> run the production step. I used the following command.. >> >> g_dist -s md_0_1.tpr -f md_0_1.xtc -o dist.xvg -n index.ndx >> >> Groups I selected was >> Group 1 (protein) >> Group 13 (ligand) >> >> It says the following error >> >> Molecule in topology has atom numbers below and above natoms (11793). >> You are probably trying to use a trajectory which does not match the first >> 11793 atoms of the run input file. >> >> how to debug the error... >> >> -- >> >> Thanking You with Regards. >> >> Arunima Shilpi >> >> Ph. D Research Scholar(Cancer & Epigenetics) >> Department of Life Science >> National Institute of Technology >> Rourkela >> Odisha >> -- >> gmx-users mailing list > >> gmx-users@ > >> 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-request@ > >> . >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > Did you check that this "You are probably trying to use a trajectory which > does not match the first > 11793 atoms of the run input file." is not the case? > > Andrish > > > > -- > View this message in context: > http://gromacs.5086.x6.nabble.com/error-in-running-g-dist-tp5008444p5008450.html > Sent from the GROMACS Users Forum mailing list archive at Nabble.com. > > > ------------------------------ > > Message: 7 > Date: Wed, 22 May 2013 16:30:12 +0200 > From: Mark Abraham <mark.j.abra...@gmail.com> > Subject: Re: [gmx-users] C6 & C12 parameters for non-bonded > interactions using tables > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: > <camnumarhwavrgtgp1adfsxb11cfgs9d6qdtceoda0x8vpkb...@mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > Exactly a factor of ten? Angstrom vs nm issue? > > > On Wed, May 22, 2013 at 4:09 PM, Andrish Reddy <are...@csir.co.za> wrote: > >> Greetings, >> >> I am trying to use tabulated potentials for the VdW interactions between >> TIP5P water molecules. >> I have tested my topology file to make sure that it gives reasonable >> results >> with the standard table6-12.xvg in the /top folder and C6=4*eps*sig^6 , >> C12=4*eps*sig^12. I am able to match the energies with an identical run >> not >> using look-up tables. The problem comes when I want to include the C6 & C12 >> parameters within the table. This is needed for dealing with more complex >> multi-parameter potential functions. >> >> I tried testing this with the standard Lennard-Jones potential. Setting >> g(r)=-(4*eps*sig^6)/r^6 and h(r)=(4*eps*sig^12)/r^12. I then construct my >> table according to [r,f(r),-f'(r),g(r),-g'(r),h(r),-h'(r)] >> >> I set vdw-type = user in my mdp file and modified my topology so that: >> [ defaults ] >> ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ >> 1 1 yes 0.5 0.8333 >> >> [ atomtypes ] >> ; name at.num mass charge ptype C6 C12 >> OW_tip5p 8 16.00 0.0000 A 1.00000e+00 1.00000e+00 >> >> Since C6 & C12 = 1, this run should be identical to using the table6-12.xvg >> and C6=4*eps*sig^6 , C12=4*eps*sig^12 >> The run proceeds fine with no warnings or errors, but the LJ and Potential >> energies are an order of magnitude higher than when using the standard >> table. I don't understand why I am not able to reproduce the results by >> this >> method? >> >> Thanks, >> Andrish >> >> >> >> >> -- >> View this message in context: >> http://gromacs.5086.x6.nabble.com/C6-C12-parameters-for-non-bonded-interactions-using-tables-tp5008449.html >> Sent from the GROMACS Users Forum mailing list archive at Nabble.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 >> > > > ------------------------------ > > Message: 8 > Date: Wed, 22 May 2013 14:30:20 +0000 > From: <l....@utwente.nl> > Subject: [gmx-users] COM coordinate fix > To: <gmx-users@gromacs.org> > Message-ID: > <64b664d3f8234d4fa8c0ba7f66fedbd03122c...@exmbx22.ad.utwente.nl> > Content-Type: text/plain; charset="iso-8859-1" > > Dear all, > > We have 80 polymers in the simulation box, for some reason, we want to make > the COM of each polymer be fixed. Is this possible in Gromacs with any > command, or somewhere in the source code we can change the expression of > displacement along with time . > > Thank you very much in advance. > > Kind regards, > Li > > > ------------------------------ > > -- > 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! > > End of gmx-users Digest, Vol 109, Issue 131 > ******************************************* > -- 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
