[gmx-users] the total charge of system is not an integer
Dear users, Before energy minimization step , I performed the preprosessing step using grompp . However, there are two note that : *NOTE 1 [file topol.top, line 52]:* System has non-zero total charge: -1.50e+01 *NOTE 2 [file topol.top]:* The largest charge group contains 11 atoms. Since atoms only see each other when the centers of geometry of the charge groups they belong to are within the cut-off distance, too large charge groups can lead to serious cut-off artifacts. For efficiency and accuracy, charge group should consist of a few atoms. For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc. * PS: *TRS and EDO are not aminoacid* TRS.itp:* .. [ moleculetype ] ; Name nrexcl TRS 3 [ atoms ] ; nr type resnr resid atom cgnr charge mass 1OA 1 TRS O1 1 -0.119 15.9994 2 H 1 TRS H13 10.032 1.0080 3 CH2 1 TRS C1 10.087 14.0270 4 CCl4 1 TRS C 20.055 12.0110 5 CH2 1 TRS C3 20.049 14.0270 6OA 1 TRS O3 2 -0.205 15.9994 7 H 1 TRS H33 20.019 1.0080 8NL 1 TRS N 20.206 14.0067 9 H 1 TRS H2 20.004 1.0080 10 H 1 TRS H3 20.004 1.0080 11 H 1 TRS H1 20.004 1.0080 12 CH2 1 TRS C2 20.050 14.0270 13OA 1 TRS O2 2 -0.205 15.9994 14 H 1 TRS H23 20.019 1.0080 ... *EDO.itp* ... [ moleculetype ] ; Name nrexcl EDO 3 [ atoms ] ; nr type resnr resid atom cgnr charge mass 1OA 1 EDO OAB 1 -0.111 15.9994 2 H 1 EDO HAE 10.031 1.0080 3 CH2 1 EDO CAA 10.080 14.0270 4 CH2 1 EDO CAC 10.080 14.0270 5OA 1 EDO OAD 1 -0.111 15.9994 6 H 1 EDO HAF 10.031 1.0080 ... * topol.top:* .. ; Include water topology #include gromos43a1.ff/spc.itp #include TRS.itp #include EDO.itp .. [ molecules ] ; Compound#mols Protein_chain_A 1 Protein_chain_B 1 SOL 185 SOL 143 TRS1 EDO1 SOL 44125 * Conf.gro:* MTA/SAH NUCLEOSIDASE; 5 NUCLEOSIDASE 5354 2GLN N1 1.458 -1.158 0.739 2GLN H12 1.520 -1.083 0.763 ... 485HOHHW1 5333 0.221 -3.864 -2.291 485HOHHW2 5334 0.303 -3.946 -2.407 1TRS O1 1 -3.812 -0.471 -2.002 1TRS H13 2 -3.865 -0.443 -1.922 1TRS C1 3 -3.672 -0.469 -1.971 1TRS C4 -3.635 -0.571 -1.863 1TRS C3 5 -3.711 -0.547 -1.731 1TRS O3 6 -3.694 -0.414 -1.679 1TRS H33 7 -3.746 -0.404 -1.594 1TRS N8 -3.673 -0.705 -1.911 1TRS H2 9 -3.625 -0.725 -1.996 1TRS H3 10 -3.771 -0.707 -1.927 1TRS H1 11 -3.649 -0.774 -1.842 1TRS C2 12 -3.483 -0.573 -1.840 1TRS O2 13 -3.428 -0.445 -1.806 1TRS H23 14 -3.470 -0.412 -1.722 1EDO OAB 1 0.307 -2.792 0.149 1EDO HAE 2 0.390 -2.826 0.104 1EDO CAA 3 0.239 -2.901 0.212 1EDO CAC 4 0.111 -2.851 0.281 1EDO OAD 5 0.144 -2.763 0.388 1EDO HAF 6 0.060 -2.731 0.432 8.13100 7.04165 13.54850 0.0 0.0 -4.06550 0.0 0.0 0.0 How can I fixed these notes(note 1 and note 2)? Thanks in advance -- Ahmet YILDIRIM -- 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] the total charge of system is not an integer
Hi Ahmet, As suggested, it's better to break up your molecule into smaller charge groups. Note that charge groups don't need to have zero charge, nor integer charge. In your case, I'd suggest two COH groups for EDO, which will have zero net charge each, and for TRS I'd take the COH groups as separate charge groups. I also note that the COH groups, although chemically identical - H3NC(COH)3, right?-, have different charges. That doesn't seem proper. Hope it helps, Tsjerk 2011/3/31 ahmet yıldırım ahmedo...@gmail.com: Dear users, Before energy minimization step , I performed the preprosessing step using grompp . However, there are two note that : NOTE 1 [file topol.top, line 52]: System has non-zero total charge: -1.50e+01 NOTE 2 [file topol.top]: The largest charge group contains 11 atoms. Since atoms only see each other when the centers of geometry of the charge groups they belong to are within the cut-off distance, too large charge groups can lead to serious cut-off artifacts. For efficiency and accuracy, charge group should consist of a few atoms. For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc. PS: TRS and EDO are not aminoacid TRS.itp: .. [ moleculetype ] ; Name nrexcl TRS 3 [ atoms ] ; nr type resnr resid atom cgnr charge mass 1 OA 1 TRS O1 1 -0.119 15.9994 2 H 1 TRS H13 1 0.032 1.0080 3 CH2 1 TRS C1 1 0.087 14.0270 4 CCl4 1 TRS C 2 0.055 12.0110 5 CH2 1 TRS C3 2 0.049 14.0270 6 OA 1 TRS O3 2 -0.205 15.9994 7 H 1 TRS H33 2 0.019 1.0080 8 NL 1 TRS N 2 0.206 14.0067 9 H 1 TRS H2 2 0.004 1.0080 10 H 1 TRS H3 2 0.004 1.0080 11 H 1 TRS H1 2 0.004 1.0080 12 CH2 1 TRS C2 2 0.050 14.0270 13 OA 1 TRS O2 2 -0.205 15.9994 14 H 1 TRS H23 2 0.019 1.0080 ... EDO.itp ... [ moleculetype ] ; Name nrexcl EDO 3 [ atoms ] ; nr type resnr resid atom cgnr charge mass 1 OA 1 EDO OAB 1 -0.111 15.9994 2 H 1 EDO HAE 1 0.031 1.0080 3 CH2 1 EDO CAA 1 0.080 14.0270 4 CH2 1 EDO CAC 1 0.080 14.0270 5 OA 1 EDO OAD 1 -0.111 15.9994 6 H 1 EDO HAF 1 0.031 1.0080 ... topol.top: .. ; Include water topology #include gromos43a1.ff/spc.itp #include TRS.itp #include EDO.itp .. [ molecules ] ; Compound #mols Protein_chain_A 1 Protein_chain_B 1 SOL 185 SOL 143 TRS 1 EDO 1 SOL 44125 Conf.gro: MTA/SAH NUCLEOSIDASE; 5 NUCLEOSIDASE 5354 2GLN N 1 1.458 -1.158 0.739 2GLN H1 2 1.520 -1.083 0.763 ... 485HOH HW1 5333 0.221 -3.864 -2.291 485HOH HW2 5334 0.303 -3.946 -2.407 1TRS O1 1 -3.812 -0.471 -2.002 1TRS H13 2 -3.865 -0.443 -1.922 1TRS C1 3 -3.672 -0.469 -1.971 1TRS C 4 -3.635 -0.571 -1.863 1TRS C3 5 -3.711 -0.547 -1.731 1TRS O3 6 -3.694 -0.414 -1.679 1TRS H33 7 -3.746 -0.404 -1.594 1TRS N 8 -3.673 -0.705 -1.911 1TRS H2 9 -3.625 -0.725 -1.996 1TRS H3 10 -3.771 -0.707 -1.927 1TRS H1 11 -3.649 -0.774 -1.842 1TRS C2 12 -3.483 -0.573 -1.840 1TRS O2 13 -3.428 -0.445 -1.806 1TRS H23 14 -3.470 -0.412 -1.722 1EDO OAB 1 0.307 -2.792 0.149 1EDO HAE 2 0.390 -2.826 0.104 1EDO CAA 3 0.239 -2.901 0.212 1EDO CAC 4 0.111 -2.851 0.281 1EDO OAD 5 0.144 -2.763 0.388 1EDO HAF 6 0.060 -2.731 0.432 8.13100 7.04165 13.54850 0.0 0.0 -4.06550 0.0 0.0 0.0 How can I fixed these notes(note 1 and note 2)? Thanks in advance -- Ahmet YILDIRIM -- 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 -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands
Re: [gmx-users] the total charge of system is not an integer
On 31/03/2011 5:18 PM, ahmet y?ld?r?m wrote: Dear users, Before energy minimization step , I performed the preprosessing step using grompp . However, there are two note that : *_NOTE 1 [file topol.top, line 52]:_* System has non-zero total charge: -1.50e+01 This is an integer. See http://en.wikipedia.org/wiki/Scientific_notation#E_notation and http://www.gromacs.org/Documentation/Floating_Point_Arithmetic _*NOTE 2 [file topol.top]:*_ The largest charge group contains 11 atoms. Since atoms only see each other when the centers of geometry of the charge groups they belong to are within the cut-off distance, too large charge groups can lead to serious cut-off artifacts. For efficiency and accuracy, charge group should consist of a few atoms. For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc. See Tsjerk's email. Mark * PS: *TRS and EDO are not aminoacid* _TRS.itp:_* .. [ moleculetype ] ; Name nrexcl TRS 3 [ atoms ] ; nr type resnr resid atom cgnr charge mass 1OA 1 TRS O1 1 -0.119 15.9994 2 H 1 TRS H13 10.032 1.0080 3 CH2 1 TRS C1 10.087 14.0270 4 CCl4 1 TRS C 20.055 12.0110 5 CH2 1 TRS C3 20.049 14.0270 6OA 1 TRS O3 2 -0.205 15.9994 7 H 1 TRS H33 20.019 1.0080 8NL 1 TRS N 20.206 14.0067 9 H 1 TRS H2 20.004 1.0080 10 H 1 TRS H3 20.004 1.0080 11 H 1 TRS H1 20.004 1.0080 12 CH2 1 TRS C2 20.050 14.0270 13OA 1 TRS O2 2 -0.205 15.9994 14 H 1 TRS H23 20.019 1.0080 ... _*EDO.itp*_ ... [ moleculetype ] ; Name nrexcl EDO 3 [ atoms ] ; nr type resnr resid atom cgnr charge mass 1OA 1 EDO OAB 1 -0.111 15.9994 2 H 1 EDO HAE 10.031 1.0080 3 CH2 1 EDO CAA 10.080 14.0270 4 CH2 1 EDO CAC 10.080 14.0270 5OA 1 EDO OAD 1 -0.111 15.9994 6 H 1 EDO HAF 10.031 1.0080 ... _* topol.top:*_ .. ; Include water topology #include gromos43a1.ff/spc.itp #include TRS.itp #include EDO.itp .. [ molecules ] ; Compound#mols Protein_chain_A 1 Protein_chain_B 1 SOL 185 SOL 143 TRS1 EDO1 SOL 44125 *_ Conf.gro:_* MTA/SAH NUCLEOSIDASE; 5 NUCLEOSIDASE 5354 2GLN N1 1.458 -1.158 0.739 2GLN H12 1.520 -1.083 0.763 ... 485HOHHW1 5333 0.221 -3.864 -2.291 485HOHHW2 5334 0.303 -3.946 -2.407 1TRS O1 1 -3.812 -0.471 -2.002 1TRS H13 2 -3.865 -0.443 -1.922 1TRS C1 3 -3.672 -0.469 -1.971 1TRS C4 -3.635 -0.571 -1.863 1TRS C3 5 -3.711 -0.547 -1.731 1TRS O3 6 -3.694 -0.414 -1.679 1TRS H33 7 -3.746 -0.404 -1.594 1TRS N8 -3.673 -0.705 -1.911 1TRS H2 9 -3.625 -0.725 -1.996 1TRS H3 10 -3.771 -0.707 -1.927 1TRS H1 11 -3.649 -0.774 -1.842 1TRS C2 12 -3.483 -0.573 -1.840 1TRS O2 13 -3.428 -0.445 -1.806 1TRS H23 14 -3.470 -0.412 -1.722 1EDO OAB 1 0.307 -2.792 0.149 1EDO HAE 2 0.390 -2.826 0.104 1EDO CAA 3 0.239 -2.901 0.212 1EDO CAC 4 0.111 -2.851 0.281 1EDO OAD 5 0.144 -2.763 0.388 1EDO HAF 6 0.060 -2.731 0.432 8.13100 7.04165 13.54850 0.0 0.0 -4.06550 0.0 0.0 0.0 How can I fixed these notes(note 1 and note 2)? Thanks in advance -- Ahmet YILDIRIM -- 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: gmx-users Digest, Vol 83, Issue 217
-1.679 1TRS H33 7 -3.746 -0.404 -1.594 1TRS N8 -3.673 -0.705 -1.911 1TRS H2 9 -3.625 -0.725 -1.996 1TRS H3 10 -3.771 -0.707 -1.927 1TRS H1 11 -3.649 -0.774 -1.842 1TRS C2 12 -3.483 -0.573 -1.840 1TRS O2 13 -3.428 -0.445 -1.806 1TRS H23 14 -3.470 -0.412 -1.722 1EDO OAB 1 0.307 -2.792 0.149 1EDO HAE 2 0.390 -2.826 0.104 1EDO CAA 3 0.239 -2.901 0.212 1EDO CAC 4 0.111 -2.851 0.281 1EDO OAD 5 0.144 -2.763 0.388 1EDO HAF 6 0.060 -2.731 0.432 8.13100 7.04165 13.54850 0.0 0.0 -4.06550 0.0 0.0 0.0 How can I fixed these notes(note 1 and note 2)? Thanks in advance -- Ahmet YILDIRIM -- next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20110331/525e314f/attachment.html -- -- 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 83, Issue 217 ** -- 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] the total charge of system is not an integer
Dear Tsjerk, I will ask you one thing but please do not get angry (I know you are not a private tutor but I need your helps). How do I apply on the files (EDO.itp and TRS.itp) that you said? (or can you suggest a tutorial?) Thanks 2011/3/31 Mark Abraham mark.abra...@anu.edu.au On 31/03/2011 5:18 PM, ahmet yıldırım wrote: Dear users, Before energy minimization step , I performed the preprosessing step using grompp . However, there are two note that : *NOTE 1 [file topol.top, line 52]:* System has non-zero total charge: -1.50e+01 This is an integer. See http://en.wikipedia.org/wiki/Scientific_notation#E_notation and http://www.gromacs.org/Documentation/Floating_Point_Arithmetic *NOTE 2 [file topol.top]:* The largest charge group contains 11 atoms. Since atoms only see each other when the centers of geometry of the charge groups they belong to are within the cut-off distance, too large charge groups can lead to serious cut-off artifacts. For efficiency and accuracy, charge group should consist of a few atoms. For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc. See Tsjerk's email. Mark * PS: *TRS and EDO are not aminoacid* TRS.itp:* .. [ moleculetype ] ; Name nrexcl TRS 3 [ atoms ] ; nr type resnr resid atom cgnr charge mass 1OA 1 TRS O1 1 -0.119 15.9994 2 H 1 TRS H13 10.032 1.0080 3 CH2 1 TRS C1 10.087 14.0270 4 CCl4 1 TRS C 20.055 12.0110 5 CH2 1 TRS C3 20.049 14.0270 6OA 1 TRS O3 2 -0.205 15.9994 7 H 1 TRS H33 20.019 1.0080 8NL 1 TRS N 20.206 14.0067 9 H 1 TRS H2 20.004 1.0080 10 H 1 TRS H3 20.004 1.0080 11 H 1 TRS H1 20.004 1.0080 12 CH2 1 TRS C2 20.050 14.0270 13OA 1 TRS O2 2 -0.205 15.9994 14 H 1 TRS H23 20.019 1.0080 ... *EDO.itp* ... [ moleculetype ] ; Name nrexcl EDO 3 [ atoms ] ; nr type resnr resid atom cgnr charge mass 1OA 1 EDO OAB 1 -0.111 15.9994 2 H 1 EDO HAE 10.031 1.0080 3 CH2 1 EDO CAA 10.080 14.0270 4 CH2 1 EDO CAC 10.080 14.0270 5OA 1 EDO OAD 1 -0.111 15.9994 6 H 1 EDO HAF 10.031 1.0080 ... * topol.top:* .. ; Include water topology #include gromos43a1.ff/spc.itp #include TRS.itp #include EDO.itp .. [ molecules ] ; Compound#mols Protein_chain_A 1 Protein_chain_B 1 SOL 185 SOL 143 TRS1 EDO1 SOL 44125 * Conf.gro:* MTA/SAH NUCLEOSIDASE; 5 NUCLEOSIDASE 5354 2GLN N1 1.458 -1.158 0.739 2GLN H12 1.520 -1.083 0.763 ... 485HOHHW1 5333 0.221 -3.864 -2.291 485HOHHW2 5334 0.303 -3.946 -2.407 1TRS O1 1 -3.812 -0.471 -2.002 1TRS H13 2 -3.865 -0.443 -1.922 1TRS C1 3 -3.672 -0.469 -1.971 1TRS C4 -3.635 -0.571 -1.863 1TRS C3 5 -3.711 -0.547 -1.731 1TRS O3 6 -3.694 -0.414 -1.679 1TRS H33 7 -3.746 -0.404 -1.594 1TRS N8 -3.673 -0.705 -1.911 1TRS H2 9 -3.625 -0.725 -1.996 1TRS H3 10 -3.771 -0.707 -1.927 1TRS H1 11 -3.649 -0.774 -1.842 1TRS C2 12 -3.483 -0.573 -1.840 1TRS O2 13 -3.428 -0.445 -1.806 1TRS H23 14 -3.470 -0.412 -1.722 1EDO OAB 1 0.307 -2.792 0.149 1EDO HAE 2 0.390 -2.826 0.104 1EDO CAA 3 0.239 -2.901 0.212 1EDO CAC 4 0.111 -2.851 0.281 1EDO OAD 5 0.144 -2.763 0.388 1EDO HAF 6 0.060 -2.731 0.432 8.13100 7.04165 13.54850 0.0 0.0 -4.06550 0.0 0.0 0.0 How can I fixed these notes(note 1 and note 2)? Thanks in advance -- Ahmet YILDIRIM -- 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 -- Ahmet YILDIRIM -- 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
Re: [gmx-users] g_dipole: dipole moment autocorrelation function
On Wed, 2011-03-30 at 20:23 +0200, David van der Spoel wrote: On 2011-03-30 20.16, Nilesh Dhumal wrote: Thanks. How can I take average. summing up and dividing by the number of sims. How much long I should run the simulation. until the average converges. Nilesh On Wed, March 30, 2011 12:59 pm, David van der Spoel wrote: On 2011-03-30 18.54, Nilesh Dhumal wrote: Hello, I am trying to calculate the dipole moment autocorrelation function for my system (ionic liquid). I am using gromacs 4.0.7 version. Hello, I think you will get into some trouble when you try to calculate an autocorrelation function of property that is not continuous in time. In an ionic liquid you have contributions of the molecular dipole and contribution of the charged molecules to the dipole. The latter part is unfortunately not continuous due to jumping of the molecules over the PBCs. It depends what kind of property you want to calculate, but we experienced that simulations in the range of 50-100ns are required to reliably determine properties like the dielectric constant. The next point is that you have to save your coordinates and velocities quite often ( every 0.02ps we used) Check corresponding literature for further advice. Cheers, Flo I run the simulation for 4 ns. I run the following command to calculate the dipole moment autocorrelation function g_dipoles -f water.trr -s water.tpr -corr total -c The function is not geting converge to zero. I want to use this data for calculation of power spectra by fourier transfom of dipole moment autocorrelation function. Can you tell why its not geting converge to zero? You have to simulate at least a few 10s of ns for such slow liquids to converge. Alternatively you can average over many independent simulations (10s). Thanks Nilesh -- 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/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 -- 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 -- Florian Dommert Dipl. - Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart EMail: domm...@icp.uni-stuttgart.de Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert Tel.: +49 - (0)711 - 68563613 Fax.: +49 - (0)711 - 68563658 signature.asc Description: This is a digitally signed message part -- 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] the total charge of system is not an integer
On 31/03/2011 6:17 PM, ahmet yıldırım wrote: Dear Tsjerk, I will ask you one thing but please do not get angry (I know you are not a private tutor but I need your helps). How do I apply on the files (EDO.itp and TRS.itp) that you said? (or can you suggest a tutorial?) You'll need to become familiar with the file format, so that you know what all the columns of data mean, so you know where the charge groups are specified. Chapter 5 of the manual is your first port of call. If you have read that and still have questions about detail, please ask on the list :-) Mark 2011/3/31 Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au On 31/03/2011 5:18 PM, ahmet yıldırım wrote: Dear users, Before energy minimization step , I performed the preprosessing step using grompp . However, there are two note that : *_NOTE 1 [file topol.top, line 52]:_* System has non-zero total charge: -1.50e+01 This is an integer. See http://en.wikipedia.org/wiki/Scientific_notation#E_notation and http://www.gromacs.org/Documentation/Floating_Point_Arithmetic _*NOTE 2 [file topol.top]:*_ The largest charge group contains 11 atoms. Since atoms only see each other when the centers of geometry of the charge groups they belong to are within the cut-off distance, too large charge groups can lead to serious cut-off artifacts. For efficiency and accuracy, charge group should consist of a few atoms. For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc. See Tsjerk's email. Mark * PS: *TRS and EDO are not aminoacid* _TRS.itp:_* .. [ moleculetype ] ; Name nrexcl TRS 3 [ atoms ] ; nr type resnr resid atom cgnr charge mass 1OA 1 TRS O1 1 -0.119 15.9994 2 H 1 TRS H13 10.032 1.0080 3 CH2 1 TRS C1 10.087 14.0270 4 CCl4 1 TRS C 20.055 12.0110 5 CH2 1 TRS C3 20.049 14.0270 6OA 1 TRS O3 2 -0.205 15.9994 7 H 1 TRS H33 20.019 1.0080 8NL 1 TRS N 20.206 14.0067 9 H 1 TRS H2 20.004 1.0080 10 H 1 TRS H3 20.004 1.0080 11 H 1 TRS H1 20.004 1.0080 12 CH2 1 TRS C2 20.050 14.0270 13OA 1 TRS O2 2 -0.205 15.9994 14 H 1 TRS H23 20.019 1.0080 ... _*EDO.itp*_ ... [ moleculetype ] ; Name nrexcl EDO 3 [ atoms ] ; nr type resnr resid atom cgnr charge mass 1OA 1 EDO OAB 1 -0.111 15.9994 2 H 1 EDO HAE 10.031 1.0080 3 CH2 1 EDO CAA 10.080 14.0270 4 CH2 1 EDO CAC 10.080 14.0270 5OA 1 EDO OAD 1 -0.111 15.9994 6 H 1 EDO HAF 10.031 1.0080 ... _* topol.top:*_ .. ; Include water topology #include gromos43a1.ff/spc.itp #include TRS.itp #include EDO.itp .. [ molecules ] ; Compound#mols Protein_chain_A 1 Protein_chain_B 1 SOL 185 SOL 143 TRS1 EDO1 SOL 44125 *_ Conf.gro:_* MTA/SAH NUCLEOSIDASE; 5 NUCLEOSIDASE 5354 2GLN N1 1.458 -1.158 0.739 2GLN H12 1.520 -1.083 0.763 ... 485HOHHW1 5333 0.221 -3.864 -2.291 485HOHHW2 5334 0.303 -3.946 -2.407 1TRS O1 1 -3.812 -0.471 -2.002 1TRS H13 2 -3.865 -0.443 -1.922 1TRS C1 3 -3.672 -0.469 -1.971 1TRS C4 -3.635 -0.571 -1.863 1TRS C3 5 -3.711 -0.547 -1.731 1TRS O3 6 -3.694 -0.414 -1.679 1TRS H33 7 -3.746 -0.404 -1.594 1TRS N8 -3.673 -0.705 -1.911 1TRS H2 9 -3.625 -0.725 -1.996 1TRS H3 10 -3.771 -0.707 -1.927 1TRS H1 11 -3.649 -0.774 -1.842 1TRS C2 12 -3.483 -0.573 -1.840 1TRS O2 13 -3.428 -0.445 -1.806 1TRS H23 14 -3.470 -0.412 -1.722 1EDO OAB 1 0.307 -2.792 0.149 1EDO HAE 2 0.390 -2.826 0.104 1EDO CAA 3 0.239 -2.901 0.212 1EDO CAC 4 0.111 -2.851 0.281 1EDO OAD 5 0.144 -2.763 0.388 1EDO HAF 6 0.060 -2.731 0.432 8.13100 7.04165 13.54850 0.0 0.0 -4.06550
[gmx-users] Help with Umbrella Sampling
-1.971 1TRS C4 -3.635 -0.571 -1.863 1TRS C3 5 -3.711 -0.547 -1.731 1TRS O3 6 -3.694 -0.414 -1.679 1TRS H33 7 -3.746 -0.404 -1.594 1TRS N8 -3.673 -0.705 -1.911 1TRS H2 9 -3.625 -0.725 -1.996 1TRS H3 10 -3.771 -0.707 -1.927 1TRS H1 11 -3.649 -0.774 -1.842 1TRS C2 12 -3.483 -0.573 -1.840 1TRS O2 13 -3.428 -0.445 -1.806 1TRS H23 14 -3.470 -0.412 -1.722 1EDO OAB 1 0.307 -2.792 0.149 1EDO HAE 2 0.390 -2.826 0.104 1EDO CAA 3 0.239 -2.901 0.212 1EDO CAC 4 0.111 -2.851 0.281 1EDO OAD 5 0.144 -2.763 0.388 1EDO HAF 6 0.060 -2.731 0.432 8.13100 7.04165 13.54850 0.0 0.0 -4.06550 0.0 0.0 0.0 How can I fixed these notes(note 1 and note 2)? Thanks in advance -- Ahmet YILDIRIM -- next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20110331/525e314f/attachment.html -- -- 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 83, Issue 217 ** -- 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] g_dipole: dipole moment autocorrelation function
On 2011-03-31 09.25, Dommert Florian wrote: On Wed, 2011-03-30 at 20:23 +0200, David van der Spoel wrote: On 2011-03-30 20.16, Nilesh Dhumal wrote: Thanks. How can I take average. summing up and dividing by the number of sims. How much long I should run the simulation. until the average converges. Nilesh On Wed, March 30, 2011 12:59 pm, David van der Spoel wrote: On 2011-03-30 18.54, Nilesh Dhumal wrote: Hello, I am trying to calculate the dipole moment autocorrelation function for my system (ionic liquid). I am using gromacs 4.0.7 version. Hello, I think you will get into some trouble when you try to calculate an autocorrelation function of property that is not continuous in time. In an ionic liquid you have contributions of the molecular dipole and contribution of the charged molecules to the dipole. The latter part is unfortunately not continuous due to jumping of the molecules over the PBCs. It depends what kind of property you want to calculate, but we experienced that simulations in the range of 50-100ns are required to reliably determine properties like the dielectric constant. The next point is that you have to save your coordinates and velocities quite often ( every 0.02ps we used) Check corresponding literature for further advice. Thanks Florian, for pointing that out. I forgot about it in my previous mail. In order to compute the dielectric constant one could in principle apply constant electric fields at different strengths and then extrapolate to zero. Don't know whether that has been done. Cheers, Flo I run the simulation for 4 ns. I run the following command to calculate the dipole moment autocorrelation function g_dipoles -f water.trr -s water.tpr -corr total -c The function is not geting converge to zero. I want to use this data for calculation of power spectra by fourier transfom of dipole moment autocorrelation function. Can you tell why its not geting converge to zero? You have to simulate at least a few 10s of ns for such slow liquids to converge. Alternatively you can average over many independent simulations (10s). Thanks Nilesh -- 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/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 -- 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 -- 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/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] the total charge of system is not an integer
Hi Ahmet, Why would I get angry? :) Sending a reply to the list will not usually be taken as asking for private tutoring... As Mark pointed out, you need to get familiar with the format of the files. That's the first thing you should do if you get to the point of needing to use non standard topologies. Read the manual, look at existing files. As for the immediate question, under the [ atoms ] section is a line indicating which column denotes what. You'd need to modify the columns 'cgnr' (charge group number) and probably 'charge'. For finding proper charge groups, in general you best draw your molecule, with the charges added, and then see which atoms would almost naturally group together. TRS.itp: .. [ moleculetype ] ; Name nrexcl TRS 3 [ atoms ] ; nr type resnr resid atom cgnr charge mass 1OA 1 TRS O1 1 -0.119 15.9994 2 H 1 TRS H13 10.032 1.0080 3 CH2 1 TRS C1 10.087 14.0270 4 CCl4 1 TRS C 20.055 12.0110 5 CH2 1 TRS C3 20.049 14.0270 6OA 1 TRS O3 2 -0.205 15.9994 Hope it helps, Tsjerk 2011/3/31 ahmet yıldırım ahmedo...@gmail.com: Dear Tsjerk, I will ask you one thing but please do not get angry (I know you are not a private tutor but I need your helps). How do I apply on the files (EDO.itp and TRS.itp) that you said? (or can you suggest a tutorial?) Thanks 2011/3/31 Mark Abraham mark.abra...@anu.edu.au On 31/03/2011 5:18 PM, ahmet yıldırım wrote: Dear users, Before energy minimization step , I performed the preprosessing step using grompp . However, there are two note that : NOTE 1 [file topol.top, line 52]: System has non-zero total charge: -1.50e+01 This is an integer. See http://en.wikipedia.org/wiki/Scientific_notation#E_notation and http://www.gromacs.org/Documentation/Floating_Point_Arithmetic NOTE 2 [file topol.top]: The largest charge group contains 11 atoms. Since atoms only see each other when the centers of geometry of the charge groups they belong to are within the cut-off distance, too large charge groups can lead to serious cut-off artifacts. For efficiency and accuracy, charge group should consist of a few atoms. For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc. See Tsjerk's email. Mark PS: TRS and EDO are not aminoacid TRS.itp: .. [ moleculetype ] ; Name nrexcl TRS 3 [ atoms ] ; nr type resnr resid atom cgnr charge mass 1 OA 1 TRS O1 1 -0.119 15.9994 2 H 1 TRS H13 1 0.032 1.0080 3 CH2 1 TRS C1 1 0.087 14.0270 4 CCl4 1 TRS C 2 0.055 12.0110 5 CH2 1 TRS C3 2 0.049 14.0270 6 OA 1 TRS O3 2 -0.205 15.9994 7 H 1 TRS H33 2 0.019 1.0080 8 NL 1 TRS N 2 0.206 14.0067 9 H 1 TRS H2 2 0.004 1.0080 10 H 1 TRS H3 2 0.004 1.0080 11 H 1 TRS H1 2 0.004 1.0080 12 CH2 1 TRS C2 2 0.050 14.0270 13 OA 1 TRS O2 2 -0.205 15.9994 14 H 1 TRS H23 2 0.019 1.0080 ... EDO.itp ... [ moleculetype ] ; Name nrexcl EDO 3 [ atoms ] ; nr type resnr resid atom cgnr charge mass 1 OA 1 EDO OAB 1 -0.111 15.9994 2 H 1 EDO HAE 1 0.031 1.0080 3 CH2 1 EDO CAA 1 0.080 14.0270 4 CH2 1 EDO CAC 1 0.080 14.0270 5 OA 1 EDO OAD 1 -0.111 15.9994 6 H 1 EDO HAF 1 0.031 1.0080 ... topol.top: .. ; Include water topology #include gromos43a1.ff/spc.itp #include TRS.itp #include EDO.itp .. [ molecules ] ; Compound #mols Protein_chain_A 1 Protein_chain_B 1 SOL 185 SOL 143 TRS 1 EDO 1 SOL 44125 Conf.gro: MTA/SAH NUCLEOSIDASE; 5 NUCLEOSIDASE 5354 2GLN N 1 1.458 -1.158 0.739 2GLN H1 2 1.520 -1.083 0.763 ... 485HOH HW1 5333 0.221 -3.864 -2.291 485HOH HW2 5334 0.303 -3.946 -2.407 1TRS O1 1 -3.812 -0.471 -2.002 1TRS H13 2 -3.865 -0.443 -1.922 1TRS C1 3 -3.672 -0.469 -1.971 1TRS C 4 -3.635 -0.571 -1.863 1TRS C3 5 -3.711 -0.547 -1.731 1TRS O3 6 -3.694 -0.414 -1.679 1TRS H33 7 -3.746 -0.404 -1.594 1TRS N 8 -3.673 -0.705 -1.911 1TRS H2 9 -3.625 -0.725 -1.996 1TRS H3 10 -3.771 -0.707 -1.927 1TRS
Re: [gmx-users] g_dipole: dipole moment autocorrelation function
On Thu, 2011-03-31 at 10:39 +0200, David van der Spoel wrote: On 2011-03-31 09.25, Dommert Florian wrote: On Wed, 2011-03-30 at 20:23 +0200, David van der Spoel wrote: On 2011-03-30 20.16, Nilesh Dhumal wrote: Thanks. How can I take average. summing up and dividing by the number of sims. How much long I should run the simulation. until the average converges. Nilesh On Wed, March 30, 2011 12:59 pm, David van der Spoel wrote: On 2011-03-30 18.54, Nilesh Dhumal wrote: Hello, I am trying to calculate the dipole moment autocorrelation function for my system (ionic liquid). I am using gromacs 4.0.7 version. Hello, I think you will get into some trouble when you try to calculate an autocorrelation function of property that is not continuous in time. In an ionic liquid you have contributions of the molecular dipole and contribution of the charged molecules to the dipole. The latter part is unfortunately not continuous due to jumping of the molecules over the PBCs. It depends what kind of property you want to calculate, but we experienced that simulations in the range of 50-100ns are required to reliably determine properties like the dielectric constant. The next point is that you have to save your coordinates and velocities quite often ( every 0.02ps we used) Check corresponding literature for further advice. Thanks Florian, for pointing that out. I forgot about it in my previous mail. In order to compute the dielectric constant one could in principle apply constant electric fields at different strengths and then extrapolate to zero. Don't know whether that has been done. In the ionic liquids commmunity dielectric spectra of ILs are usually calulated from equilibrium MD without application of an E-field. The generalized dielectric constant is calculated and a Fourier Laplace transformation finally allows to determine the full dielectric spectrum. Schröder et. al from the University of Vienna have published some articles about this topic. Cheers, Flo Cheers, Flo I run the simulation for 4 ns. I run the following command to calculate the dipole moment autocorrelation function g_dipoles -f water.trr -s water.tpr -corr total -c The function is not geting converge to zero. I want to use this data for calculation of power spectra by fourier transfom of dipole moment autocorrelation function. Can you tell why its not geting converge to zero? You have to simulate at least a few 10s of ns for such slow liquids to converge. Alternatively you can average over many independent simulations (10s). Thanks Nilesh -- 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/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 -- 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 -- 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 -- Florian Dommert Dipl. - Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart EMail: domm...@icp.uni-stuttgart.de Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert Tel.: +49 - (0)711 - 68563613 Fax.: +49 - (0)711 - 68563658 signature.asc Description: This is a digitally signed message part -- 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] Umbrella sampling
Hi All I have generated several PMF curves for the one system using umbrella sampling. In the first part of the curve (barrier region) I use a high force constant with small intervals between the windows. The latter part of the curve I use a lower force constant with larger window spacing. Anyway I have a few issues that I need clarifying: 1 - Can you have too much overlap between windows? 2 - Does the distribution at each window have to centered around the desired r0? (If not does this affect the free energy?) 3- If you over sample one particular window, will it affect the curve? Many thanks GAvin -- 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] Umbrella sampling
On Mar 31, 2011, at 11:53 AM, Gavin Melaugh wrote: Hi All I have generated several PMF curves for the one system using umbrella sampling. In the first part of the curve (barrier region) I use a high force constant with small intervals between the windows. The latter part of the curve I use a lower force constant with larger window spacing. Anyway I have a few issues that I need clarifying: 1 - Can you have too much overlap between windows? no, there no such a thing of too much overlap :)) You could even put two identical windows with same 100% overlap ... no problem. 2 - Does the distribution at each window have to centered around the desired r0? (If not does this affect the free energy?) The deviation of the distribution from the r0 is what dictates the profile. The more away from the disired r0 the higher the free energy of the system. 3- If you over sample one particular window, will it affect the curve? There is no such a thing of over sampling ... the only thing you can have is not enough sampling. Many thanks GAvin -- 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 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] manually creating a topology file
Dear all, I intend to run a simulation for a membrane protein. As per a tutorial, i require a lipid bilayer and some (.itp) files for editing manually a toplogy file for the lipid bilayer. Question is how do I choose the appropriate lipid bilayer and its subsequent (.itp) file? Also, what are the required necessary things to be edited. I intend to use teh OPLS-AA force field to represent my protein -- Nishith Saurav Topno -- 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] Umbrella sampling
Hi Xavier Thanks for the reply. With respect to your answer of my first query. What if you had two windows practically on top of each other, but one was not supposed to be there. e.g A window with r0 of 0.80 nm and centred at 0.78 nm and a window with r0 of 0.78 nm centred at 0.78nm. Gavin XAvier Periole wrote: On Mar 31, 2011, at 11:53 AM, Gavin Melaugh wrote: Hi All I have generated several PMF curves for the one system using umbrella sampling. In the first part of the curve (barrier region) I use a high force constant with small intervals between the windows. The latter part of the curve I use a lower force constant with larger window spacing. Anyway I have a few issues that I need clarifying: 1 - Can you have too much overlap between windows? no, there no such a thing of too much overlap :)) You could even put two identical windows with same 100% overlap ... no problem. 2 - Does the distribution at each window have to centered around the desired r0? (If not does this affect the free energy?) The deviation of the distribution from the r0 is what dictates the profile. The more away from the disired r0 the higher the free energy of the system. 3- If you over sample one particular window, will it affect the curve? There is no such a thing of over sampling ... the only thing you can have is not enough sampling. Many thanks GAvin -- 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 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] Help with Umbrella Sampling
Raghuvir R S Pissurlenkar wrote: Dear Justin I removed the constrain on the DPPC molecules, however I find still LINCS errors are prominent Any alterative can I try Reduce the pull_rate. If you pull too fast, your system cannot adapt properly to the collisions that are induced by the artificial force. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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] manually creating a topology file
On 31/03/11, Nishith Saurav Topno nto...@bicpu.edu.in wrote: Dear all, I intend to run a simulation for a membrane protein. As per a tutorial, i require a lipid bilayer and some (.itp) files for editing manually a toplogy file for the lipid bilayer. Question is how do I choose the appropriate lipid bilayer and its subsequent (.itp) file? That depends on what you are modelling and what you are hoping to observe. There's no substitute for knowledge and learning about the biochemical system of interest, and how other people have approached similar problems, and what they learned. Also, what are the required necessary things to be edited. I intend to use teh OPLS-AA force field to represent my protein That sounds like you are pre-supposing the use of a particular tool. A better approach is to look at published studies similar to the one you propose, to learn from their apparent successes and failures, and to choose tools and methods accordingly. Having chosen tools and methods, it is certain that you will need to spend time reading tutorials, documentation, published articles and asking questions of experts. Indeed, if you can't do this, then you should probably revisit those chocies of tools and methods, or even the proposed study. 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
[gmx-users] gromacs/CPMD. Is LAM mandatory?
Dear all, I am trying to do a QM/MM calculation with gromacs/CPMD. When I try to use a parallel version of mdrun and CPMD I get a segmentation fault. I have seen in the examples that LAM is used in runcpmd. It is mandatory for parallel runs? I do not have this problem when I run just CPMD in parallel Regards *** Elena ETH Zürich and Università della Svizzera Italiana, USI -- 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] Umbrella sampling
You can present the data differently: you have two windows at 0.78 nm giving different distribution. That indicates these windows are not converged. Does not mean that the others (0.80 nm) are converged :)) On Mar 31, 2011, at 12:20 PM, Gavin Melaugh wrote: Hi Xavier Thanks for the reply. With respect to your answer of my first query. What if you had two windows practically on top of each other, but one was not supposed to be there. e.g A window with r0 of 0.80 nm and centred at 0.78 nm and a window with r0 of 0.78 nm centred at 0.78nm. Gavin XAvier Periole wrote: On Mar 31, 2011, at 11:53 AM, Gavin Melaugh wrote: Hi All I have generated several PMF curves for the one system using umbrella sampling. In the first part of the curve (barrier region) I use a high force constant with small intervals between the windows. The latter part of the curve I use a lower force constant with larger window spacing. Anyway I have a few issues that I need clarifying: 1 - Can you have too much overlap between windows? no, there no such a thing of too much overlap :)) You could even put two identical windows with same 100% overlap ... no problem. 2 - Does the distribution at each window have to centered around the desired r0? (If not does this affect the free energy?) The deviation of the distribution from the r0 is what dictates the profile. The more away from the disired r0 the higher the free energy of the system. 3- If you over sample one particular window, will it affect the curve? There is no such a thing of over sampling ... the only thing you can have is not enough sampling. Many thanks GAvin -- 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 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 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] gromacs/CPMD. Is LAM mandatory?
On 31/03/11, Elena Formoso elena.form...@phys.chem.ethz.ch wrote: Dear all, I am trying to do a QM/MM calculation with gromacs/CPMD. When I try to use a parallel version of mdrun and CPMD I get a segmentation fault. I have seen in the examples that LAM is used in runcpmd. It is mandatory for parallel runs? LAM is a deprecated library implementing the MPI standard. Whether it is necessary, or another MPI implementation is possible (or even preferable) is a question that should be answered in the documentation of the GROMACS-CPMD port. Is it? 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] Umbrella sampling
Sorry I am not sure that I follow. Will the window with r0 =0.80 giving the distribution centred around 0.78nm not drive my free energy profile up. If I remove this window prior to running g_wham the free energy goes down. Should I increase the force constant so that the mean of the window is 0.80nm (bearing in mind that this is near the barrier region). Gavin XAvier Periole wrote: You can present the data differently: you have two windows at 0.78 nm giving different distribution. That indicates these windows are not converged. Does not mean that the others (0.80 nm) are converged :)) On Mar 31, 2011, at 12:20 PM, Gavin Melaugh wrote: Hi Xavier Thanks for the reply. With respect to your answer of my first query. What if you had two windows practically on top of each other, but one was not supposed to be there. e.g A window with r0 of 0.80 nm and centred at 0.78 nm and a window with r0 of 0.78 nm centred at 0.78nm. Gavin XAvier Periole wrote: On Mar 31, 2011, at 11:53 AM, Gavin Melaugh wrote: Hi All I have generated several PMF curves for the one system using umbrella sampling. In the first part of the curve (barrier region) I use a high force constant with small intervals between the windows. The latter part of the curve I use a lower force constant with larger window spacing. Anyway I have a few issues that I need clarifying: 1 - Can you have too much overlap between windows? no, there no such a thing of too much overlap :)) You could even put two identical windows with same 100% overlap ... no problem. 2 - Does the distribution at each window have to centered around the desired r0? (If not does this affect the free energy?) The deviation of the distribution from the r0 is what dictates the profile. The more away from the disired r0 the higher the free energy of the system. 3- If you over sample one particular window, will it affect the curve? There is no such a thing of over sampling ... the only thing you can have is not enough sampling. Many thanks GAvin -- 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 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 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] gromacs/CPMD. Is LAM mandatory?
Hi Elena, if you use GMX/CPMD in parallel, you can use any mpi implementation, but you should start GMX on a single core and CPMD in parallel (via runcpmd). You can not run both in parallel. Greets, Christian On Thu, 2011-03-31 at 13:05 +0200, Elena Formoso wrote: Dear all, I am trying to do a QM/MM calculation with gromacs/CPMD. When I try to use a parallel version of mdrun and CPMD I get a segmentation fault. I have seen in the examples that LAM is used in runcpmd. It is mandatory for parallel runs? I do not have this problem when I run just CPMD in parallel Regards *** Elena ETH Zürich and Università della Svizzera Italiana, USI -- 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 -- M.Sc. Christian Seifert Department of Biophysics University of Bochum ND 04/67 44780 Bochum Germany Tel: +49 (0)234 32 28363 Fax: +49 (0)234 32 14626 E-Mail: cseif...@bph.rub.de Web: http://www.bph.rub.de -- 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] gromacs/CPMD. Is LAM mandatory?
Thanks Christian That is why it was not working. It is not possible to run both in parallel Cheers Elena On Thu, Mar 31, 2011 at 1:14 PM, Christian Seifert cseif...@bph.ruhr-uni-bochum.de wrote: Hi Elena, if you use GMX/CPMD in parallel, you can use any mpi implementation, but you should start GMX on a single core and CPMD in parallel (via runcpmd). You can not run both in parallel. Greets, Christian On Thu, 2011-03-31 at 13:05 +0200, Elena Formoso wrote: Dear all, I am trying to do a QM/MM calculation with gromacs/CPMD. When I try to use a parallel version of mdrun and CPMD I get a segmentation fault. I have seen in the examples that LAM is used in runcpmd. It is mandatory for parallel runs? I do not have this problem when I run just CPMD in parallel Regards *** Elena ETH Zürich and Università della Svizzera Italiana, USI -- 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 -- M.Sc. Christian Seifert Department of Biophysics University of Bochum ND 04/67 44780 Bochum Germany Tel: +49 (0)234 32 28363 Fax: +49 (0)234 32 14626 E-Mail: cseif...@bph.rub.de Web: http://www.bph.rub.de -- 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 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] Umbrella sampling
Gavin Melaugh wrote: Sorry I am not sure that I follow. Will the window with r0 =0.80 giving the distribution centred around 0.78nm not drive my free energy profile up. If I remove this window prior to running g_wham the free energy goes down. Should I increase the force constant so that the mean of the window is 0.80nm (bearing in mind that this is near the barrier region). If you have an incomplete or otherwise discontinuous free energy profile, then you won't get a correct result, but it's not simply due to oversampling one region. It's that the oversampling results in undersampling another region. Increasing the force constant for the window centered around 0.80 nm should work. -Justin Gavin XAvier Periole wrote: You can present the data differently: you have two windows at 0.78 nm giving different distribution. That indicates these windows are not converged. Does not mean that the others (0.80 nm) are converged :)) On Mar 31, 2011, at 12:20 PM, Gavin Melaugh wrote: Hi Xavier Thanks for the reply. With respect to your answer of my first query. What if you had two windows practically on top of each other, but one was not supposed to be there. e.g A window with r0 of 0.80 nm and centred at 0.78 nm and a window with r0 of 0.78 nm centred at 0.78nm. Gavin XAvier Periole wrote: On Mar 31, 2011, at 11:53 AM, Gavin Melaugh wrote: Hi All I have generated several PMF curves for the one system using umbrella sampling. In the first part of the curve (barrier region) I use a high force constant with small intervals between the windows. The latter part of the curve I use a lower force constant with larger window spacing. Anyway I have a few issues that I need clarifying: 1 - Can you have too much overlap between windows? no, there no such a thing of too much overlap :)) You could even put two identical windows with same 100% overlap ... no problem. 2 - Does the distribution at each window have to centered around the desired r0? (If not does this affect the free energy?) The deviation of the distribution from the r0 is what dictates the profile. The more away from the disired r0 the higher the free energy of the system. 3- If you over sample one particular window, will it affect the curve? There is no such a thing of over sampling ... the only thing you can have is not enough sampling. Many thanks GAvin -- 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 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 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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] CUT-OFFs for GROMOS96 43a1...Reg
Dear All, I am running MD simulations of an Alcohol Dehydrogenase ( a tetramer) with the bound NADPH in explicit solvent. I am employing GROMOS96 43a1 force field for the simulations. I need a clarification on the CUT-OFFs applicable for this force field. I have seen many people using *rvdw = 1.4* and*rcoulomb = 1.0 ( short range vander-waals and elctrostatics cut-offs) *in all the .mdp files. In the tutorial I am following (Justin Lemkul's - protein ligand complex)) he used *rvdw = 1.0* and *rcoulomb = 1.0* in case of energy minimisation and* rvdw = 1.4* and *rcoulomb = 0.9* in case of NVT/NPT equilibration and production MD run. So, someone please clarify me what the widely accepted values for these two would be. If at all I should use* rvdw = 1.4*, then should -d flag in editconf be atleast 1.4 or can it be less than that in the case of PBC conditions enabled. -- KRISHNA KISHORE@IIT-MADRAS -- 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] Umbrella sampling
Thanks Justin for the reply Gavin Justin A. Lemkul wrote: Gavin Melaugh wrote: Sorry I am not sure that I follow. Will the window with r0 =0.80 giving the distribution centred around 0.78nm not drive my free energy profile up. If I remove this window prior to running g_wham the free energy goes down. Should I increase the force constant so that the mean of the window is 0.80nm (bearing in mind that this is near the barrier region). If you have an incomplete or otherwise discontinuous free energy profile, then you won't get a correct result, but it's not simply due to oversampling one region. It's that the oversampling results in undersampling another region. Increasing the force constant for the window centered around 0.80 nm should work. -Justin Gavin XAvier Periole wrote: You can present the data differently: you have two windows at 0.78 nm giving different distribution. That indicates these windows are not converged. Does not mean that the others (0.80 nm) are converged :)) On Mar 31, 2011, at 12:20 PM, Gavin Melaugh wrote: Hi Xavier Thanks for the reply. With respect to your answer of my first query. What if you had two windows practically on top of each other, but one was not supposed to be there. e.g A window with r0 of 0.80 nm and centred at 0.78 nm and a window with r0 of 0.78 nm centred at 0.78nm. Gavin XAvier Periole wrote: On Mar 31, 2011, at 11:53 AM, Gavin Melaugh wrote: Hi All I have generated several PMF curves for the one system using umbrella sampling. In the first part of the curve (barrier region) I use a high force constant with small intervals between the windows. The latter part of the curve I use a lower force constant with larger window spacing. Anyway I have a few issues that I need clarifying: 1 - Can you have too much overlap between windows? no, there no such a thing of too much overlap :)) You could even put two identical windows with same 100% overlap ... no problem. 2 - Does the distribution at each window have to centered around the desired r0? (If not does this affect the free energy?) The deviation of the distribution from the r0 is what dictates the profile. The more away from the disired r0 the higher the free energy of the system. 3- If you over sample one particular window, will it affect the curve? There is no such a thing of over sampling ... the only thing you can have is not enough sampling. Many thanks GAvin -- 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 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 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] CUT-OFFs for GROMOS96 43a1...Reg
Kishore wrote: Dear All, I am running MD simulations of an Alcohol Dehydrogenase ( a tetramer) with the bound NADPH in explicit solvent. I am employing GROMOS96 43a1 force field for the simulations. I need a clarification on the CUT-OFFs applicable for this force field. I have seen many people using *rvdw = 1.4* and* rcoulomb = 1.0 ( short range vander-waals and elctrostatics cut-offs) *in all the .mdp files. In the tutorial I am following (Justin Lemkul's - protein ligand complex)) he used *rvdw = 1.0* and *rcoulomb = 1.0* in case of energy minimisation and* rvdw = 1.4* and *rcoulomb = 0.9* in case of NVT/NPT equilibration and production MD run. So, someone please clarify me what the widely accepted values for these two would be. If at all I should use* rvdw = 1.4*, then should -d flag in editconf The latter. EM is relatively insensitive to the cutoffs in my experience, so 1.0 is fine there. For the real MD, use the proper settings given in the production MD .mdp file. be atleast 1.4 or can it be less than that in the case of PBC conditions enabled. You simply have to ensure that your system's components never see one another. In principle, you'd be safe setting -d 1.4 and have a maximum of 2.8 nm between periodic images. That can result in a lot of wasted time doing calculations on distant water molecules when the box size gets extremely large. If the box size/shape will not change much (as is the case for most well-equilibrated protein/water systems), you can get away with a shorter value of -d, maybe 1.0 or so. Don't set it as low as 0.7 (such that the periodic distance is exactly 1.4 nm, equal to the cutoff), because then any small fluctuation can cause you problems. -Justin -- KRISHNA KISHORE@IIT-MADRAS -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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] Umbrella sampling
My bad, I red to quick and though you had three windows ... you should follow Justin's advice. On Mar 31, 2011, at 2:20 PM, Gavin Melaugh wrote: Thanks Justin for the reply Gavin Justin A. Lemkul wrote: Gavin Melaugh wrote: Sorry I am not sure that I follow. Will the window with r0 =0.80 giving the distribution centred around 0.78nm not drive my free energy profile up. If I remove this window prior to running g_wham the free energy goes down. Should I increase the force constant so that the mean of the window is 0.80nm (bearing in mind that this is near the barrier region). If you have an incomplete or otherwise discontinuous free energy profile, then you won't get a correct result, but it's not simply due to oversampling one region. It's that the oversampling results in undersampling another region. Increasing the force constant for the window centered around 0.80 nm should work. -Justin Gavin XAvier Periole wrote: You can present the data differently: you have two windows at 0.78 nm giving different distribution. That indicates these windows are not converged. Does not mean that the others (0.80 nm) are converged :)) On Mar 31, 2011, at 12:20 PM, Gavin Melaugh wrote: Hi Xavier Thanks for the reply. With respect to your answer of my first query. What if you had two windows practically on top of each other, but one was not supposed to be there. e.g A window with r0 of 0.80 nm and centred at 0.78 nm and a window with r0 of 0.78 nm centred at 0.78nm. Gavin XAvier Periole wrote: On Mar 31, 2011, at 11:53 AM, Gavin Melaugh wrote: Hi All I have generated several PMF curves for the one system using umbrella sampling. In the first part of the curve (barrier region) I use a high force constant with small intervals between the windows. The latter part of the curve I use a lower force constant with larger window spacing. Anyway I have a few issues that I need clarifying: 1 - Can you have too much overlap between windows? no, there no such a thing of too much overlap :)) You could even put two identical windows with same 100% overlap ... no problem. 2 - Does the distribution at each window have to centered around the desired r0? (If not does this affect the free energy?) The deviation of the distribution from the r0 is what dictates the profile. The more away from the disired r0 the higher the free energy of the system. 3- If you over sample one particular window, will it affect the curve? There is no such a thing of over sampling ... the only thing you can have is not enough sampling. Many thanks GAvin -- 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 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 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 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] g_dipole: dipole moment autocorrelation function
Thanks Flo for detail reply. Is it possible to put PBC off during calculation of dipole moment autocorrelation function. I will run the simulation for 50ns ans try to save trajectroy of 0.02ps. Thanks NIlesh Nilesh On Thu, March 31, 2011 5:38 am, Dommert Florian wrote: On Thu, 2011-03-31 at 10:39 +0200, David van der Spoel wrote: On 2011-03-31 09.25, Dommert Florian wrote: On Wed, 2011-03-30 at 20:23 +0200, David van der Spoel wrote: On 2011-03-30 20.16, Nilesh Dhumal wrote: Thanks. How can I take average. summing up and dividing by the number of sims. How much long I should run the simulation. until the average converges. Nilesh On Wed, March 30, 2011 12:59 pm, David van der Spoel wrote: On 2011-03-30 18.54, Nilesh Dhumal wrote: Hello, I am trying to calculate the dipole moment autocorrelation function for my system (ionic liquid). I am using gromacs 4.0.7 version. Hello, I think you will get into some trouble when you try to calculate an autocorrelation function of property that is not continuous in time. In an ionic liquid you have contributions of the molecular dipole and contribution of the charged molecules to the dipole. The latter part is unfortunately not continuous due to jumping of the molecules over the PBCs. It depends what kind of property you want to calculate, but we experienced that simulations in the range of 50-100ns are required to reliably determine properties like the dielectric constant. The next point is that you have to save your coordinates and velocities quite often ( every 0.02ps we used) Check corresponding literature for further advice. Thanks Florian, for pointing that out. I forgot about it in my previous mail. In order to compute the dielectric constant one could in principle apply constant electric fields at different strengths and then extrapolate to zero. Don't know whether that has been done. In the ionic liquids commmunity dielectric spectra of ILs are usually calulated from equilibrium MD without application of an E-field. The generalized dielectric constant is calculated and a Fourier Laplace transformation finally allows to determine the full dielectric spectrum. Schröder et. al from the University of Vienna have published some articles about this topic. Cheers, Flo Cheers, Flo I run the simulation for 4 ns. I run the following command to calculate the dipole moment autocorrelation function g_dipoles -f water.trr -s water.tpr -corr total -c The function is not geting converge to zero. I want to use this data for calculation of power spectra by fourier transfom of dipole moment autocorrelation function. Can you tell why its not geting converge to zero? You have to simulate at least a few 10s of ns for such slow liquids to converge. Alternatively you can average over many independent simulations (10s). Thanks Nilesh -- 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/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 -- 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 -- 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 -- Florian Dommert Dipl. - Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart EMail: domm...@icp.uni-stuttgart.de Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert Tel.: +49 - (0)711 - 68563613 Fax.: +49 - (0)711 - 68563658 -- 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 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?
Re: [gmx-users] g_dipole: dipole moment autocorrelation function
On Thu, 2011-03-31 at 08:53 -0400, Nilesh Dhumal wrote: Thanks Flo for detail reply. Is it possible to put PBC off during calculation of dipole moment autocorrelation function. No, thats the problem, because the volume of the system will increase and dipole density will decrease, this not what you want. However I've written the tool g_current, that allows to calculate the dielectric constant and terms of which it is composed. Read our paper (DOI: 10.1063/1.3030948), which describes the procedure and look at the help, what the programm can do. Cheers, Flo I will run the simulation for 50ns ans try to save trajectroy of 0.02ps. Thanks NIlesh Nilesh On Thu, March 31, 2011 5:38 am, Dommert Florian wrote: On Thu, 2011-03-31 at 10:39 +0200, David van der Spoel wrote: On 2011-03-31 09.25, Dommert Florian wrote: On Wed, 2011-03-30 at 20:23 +0200, David van der Spoel wrote: On 2011-03-30 20.16, Nilesh Dhumal wrote: Thanks. How can I take average. summing up and dividing by the number of sims. How much long I should run the simulation. until the average converges. Nilesh On Wed, March 30, 2011 12:59 pm, David van der Spoel wrote: On 2011-03-30 18.54, Nilesh Dhumal wrote: Hello, I am trying to calculate the dipole moment autocorrelation function for my system (ionic liquid). I am using gromacs 4.0.7 version. Hello, I think you will get into some trouble when you try to calculate an autocorrelation function of property that is not continuous in time. In an ionic liquid you have contributions of the molecular dipole and contribution of the charged molecules to the dipole. The latter part is unfortunately not continuous due to jumping of the molecules over the PBCs. It depends what kind of property you want to calculate, but we experienced that simulations in the range of 50-100ns are required to reliably determine properties like the dielectric constant. The next point is that you have to save your coordinates and velocities quite often ( every 0.02ps we used) Check corresponding literature for further advice. Thanks Florian, for pointing that out. I forgot about it in my previous mail. In order to compute the dielectric constant one could in principle apply constant electric fields at different strengths and then extrapolate to zero. Don't know whether that has been done. In the ionic liquids commmunity dielectric spectra of ILs are usually calulated from equilibrium MD without application of an E-field. The generalized dielectric constant is calculated and a Fourier Laplace transformation finally allows to determine the full dielectric spectrum. Schröder et. al from the University of Vienna have published some articles about this topic. Cheers, Flo Cheers, Flo I run the simulation for 4 ns. I run the following command to calculate the dipole moment autocorrelation function g_dipoles -f water.trr -s water.tpr -corr total -c The function is not geting converge to zero. I want to use this data for calculation of power spectra by fourier transfom of dipole moment autocorrelation function. Can you tell why its not geting converge to zero? You have to simulate at least a few 10s of ns for such slow liquids to converge. Alternatively you can average over many independent simulations (10s). Thanks Nilesh -- 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/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 -- 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 -- 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 -- Florian Dommert Dipl. - Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart EMail: domm...@icp.uni-stuttgart.de Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert Tel.: +49 - (0)711 - 68563613 Fax.: +49 - (0)711 - 68563658 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users
[gmx-users] converting ILDN parameters to RB
Hi there, Since ILDN dihedrals has some parameters with up to periodicity 6, I was wondering if it's possible to convert it in RB with 6 coefficients. If so, what would be the formula? For example, for converting the usual Amber99SB to RB I have: if phase in [0, 180]: if kPhi 0: V[period] = 2 * kPhi * cal if period == 1: C[0] += 0.5 * V[period] if phase == 0: C[1] -= 0.5 * V[period] else: C[1] += 0.5 * V[period] elif period == 2: if phase == 180: C[0] += V[period] C[2] -= V[period] else: C[2] += V[period] elif period == 3: C[0] += 0.5 * V[period] if phase == 0: C[1] += 1.5 * V[period] C[3] -= 2 * V[period] else: C[1] -= 1.5 * V[period] C[3] += 2 * V[period] elif period == 4: if phase == 180: C[2] += 4 * V[period] C[4] -= 4 * V[period] else: C[0] += V[period] C[2] -= 4 * V[period] C[4] += 4 * V[period] So, as you can see, I can handle up to 4 periods (C[5] is always 0, but not with ILDN and I need to add C[6] rules as well). Any ideas? Many thanks in advance, Alan -- Alan Wilter SOUSA da SILVA, DSc Bioinformatician, UniProt - PANDA, EMBL-EBI CB10 1SD, Hinxton, Cambridge, UK +44 1223 49 4588 -- 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] couple-moltype for two molecules
Dear all, I tryed to use couple-moltype=Protein Ligand directive to annihilate both protein and ligand molecules using free energy method. I realized that couple-moltype key works for only one molecule type. Is it right? To perform the same annihilation I used couple-moltype=Protein to annihilate the protein and dual topology formalism (definied in itp file) to annihilate the ligand. Are these commands able to work together? Thanks Luca -- 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] couple-moltype for two molecules
Dear all, I tryed to use couple-moltype=Protein Ligand directive to annihilate both protein and ligand molecules using free energy method. I realized that couple-moltype key works for only one molecule type. Is it right? To perform the same annihilation I used couple-moltype=Protein to annihilate the protein and dual topology formalism (definied in itp file) to annihilate the ligand. Are these commands able to work together? Thanks Luca -- 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] couple-moltype for two molecules
Dear all, I tryed to use couple-moltype=Protein Ligand directive to annihilate both protein and ligand molecules using free energy method. I realized that couple-moltype key works for only one molecule type. Is it right? To perform the same annihilation I used couple-moltype=Protein to annihilate the protein and dual topology formalism (definied in itp file) to annihilate the ligand. Are these commands able to work together? Thanks Luca -- 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] converting ILDN parameters to RB
I know it's supported. I was just investigating the possibility since I build acpype to create topologies for gromacs, but also it converts from amber to gromacs (like amb2gmx.pl), and so I was wondering about RB with 6 coefficients since multiple proper dihedrals is only supported for gmx 4.5 and above. But I don't want to fuss about it. If to forget about GMX 4.0.x and below is the way, so it will be. Thanks, Alan On 31 March 2011 16:08, David van der Spoel sp...@xray.bmc.uu.se wrote: On 2011-03-31 15.27, Alan Wilter Sousa da Silva wrote: Hi there, Since ILDN dihedrals has some parameters with up to periodicity 6, I was wondering if it's possible to convert it in RB with 6 coefficients. If so, what would be the formula? For example, for converting the usual Amber99SB to RB I have: ILDN is already supported in the latest gromacs releases, by simply using multiple proper dihedrals. Why would you want to change it? if phase in [0, 180]: if kPhi 0: V[period] = 2 * kPhi * cal if period == 1: C[0] += 0.5 * V[period] if phase == 0: C[1] -= 0.5 * V[period] else: C[1] += 0.5 * V[period] elif period == 2: if phase == 180: C[0] += V[period] C[2] -= V[period] else: C[2] += V[period] elif period == 3: C[0] += 0.5 * V[period] if phase == 0: C[1] += 1.5 * V[period] C[3] -= 2 * V[period] else: C[1] -= 1.5 * V[period] C[3] += 2 * V[period] elif period == 4: if phase == 180: C[2] += 4 * V[period] C[4] -= 4 * V[period] else: C[0] += V[period] C[2] -= 4 * V[period] C[4] += 4 * V[period] So, as you can see, I can handle up to 4 periods (C[5] is always 0, but not with ILDN and I need to add C[6] rules as well). Any ideas? Many thanks in advance, Alan -- Alan Wilter SOUSA da SILVA, DSc Bioinformatician, UniProt - PANDA, EMBL-EBI CB10 1SD, Hinxton, Cambridge, UK +44 1223 49 4588 -- 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/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 -- Alan Wilter SOUSA da SILVA, DSc Bioinformatician, UniProt - PANDA, EMBL-EBI CB10 1SD, Hinxton, Cambridge, UK +44 1223 49 4588 -- 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] converting ILDN parameters to RB
On 2011-03-31 17.19, Alan Wilter Sousa da Silva wrote: I know it's supported. I was just investigating the possibility since I build acpype to create topologies for gromacs, but also it converts from amber to gromacs (like amb2gmx.pl http://amb2gmx.pl), and so I was wondering about RB with 6 coefficients since multiple proper dihedrals is only supported for gmx 4.5 and above. Unfortunately RB only goes to 5 and it would be a pain to support more since the tpr format would have to be updated. The current solution with the type 9 dihedrals is a royal pain in the neck too. I've actually written a script that converts the present rtp files to contain *all* bonded interactions explicitly (with parameters), and it replaces the 9 type dihedrals with multiple 1 type dihedrals (lots of them with all zeros, LOL). But I don't want to fuss about it. If to forget about GMX 4.0.x and below is the way, so it will be. Thanks, Alan On 31 March 2011 16:08, David van der Spoel sp...@xray.bmc.uu.se mailto:sp...@xray.bmc.uu.se wrote: On 2011-03-31 15.27, Alan Wilter Sousa da Silva wrote: Hi there, Since ILDN dihedrals has some parameters with up to periodicity 6, I was wondering if it's possible to convert it in RB with 6 coefficients. If so, what would be the formula? For example, for converting the usual Amber99SB to RB I have: ILDN is already supported in the latest gromacs releases, by simply using multiple proper dihedrals. Why would you want to change it? if phase in [0, 180]: if kPhi 0: V[period] = 2 * kPhi * cal if period == 1: C[0] += 0.5 * V[period] if phase == 0: C[1] -= 0.5 * V[period] else: C[1] += 0.5 * V[period] elif period == 2: if phase == 180: C[0] += V[period] C[2] -= V[period] else: C[2] += V[period] elif period == 3: C[0] += 0.5 * V[period] if phase == 0: C[1] += 1.5 * V[period] C[3] -= 2 * V[period] else: C[1] -= 1.5 * V[period] C[3] += 2 * V[period] elif period == 4: if phase == 180: C[2] += 4 * V[period] C[4] -= 4 * V[period] else: C[0] += V[period] C[2] -= 4 * V[period] C[4] += 4 * V[period] So, as you can see, I can handle up to 4 periods (C[5] is always 0, but not with ILDN and I need to add C[6] rules as well). Any ideas? Many thanks in advance, Alan -- Alan Wilter SOUSA da SILVA, DSc Bioinformatician, UniProt - PANDA, EMBL-EBI CB10 1SD, Hinxton, Cambridge, UK +44 1223 49 4588 -- 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.se mailto:sp...@xray.bmc.uu.se http://folding.bmc.uu.se -- gmx-users mailing list gmx-users@gromacs.org mailto: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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Alan Wilter SOUSA da SILVA, DSc Bioinformatician, UniProt - PANDA, EMBL-EBI CB10 1SD, Hinxton, Cambridge, UK +44 1223 49 4588 -- 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/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] Umbrella sampling
can you show us your mdp and the pmf and the histograms for the data that you put into wham? It's a lot easier to diagnose with the real data. In the general case where umbrellas are spaced equally along your reaction coordinate, sampling overlap between umbrellas will always decrease anywhere the PMF is concave down, such as your barrier region. I would suggest adding windows at every 0.005 nm spanning the region that you consider to have a sampling problem (e.g. 0.76 to 0.83 ?) and use a much stronger force constant here (e.g. 2-3 times as strong as you used for umbrellas with 0.02 nm spacing). You have identified a problem, so my suggestion is to not bother fiddling with adding one extra replica but sample that region to death with strong force constants. I presume that this will not impact your overall efficiency too much if the reaction coordinate is long overall. Finally, you will need to evaluate the convergence of your PMF overall and perhaps of this region in particular, especially if you want to know the dG to cross it or between two low energy states on either side of it. Chris. -- original message -- Sorry I am not sure that I follow. Will the window with r0 =0.80 giving the distribution centred around 0.78nm not drive my free energy profile up. If I remove this window prior to running g_wham the free energy goes down. Should I increase the force constant so that the mean of the window is 0.80nm (bearing in mind that this is near the barrier region). Gavin XAvier Periole wrote: You can present the data differently: you have two windows at 0.78 nm giving different distribution. That indicates these windows are not converged. Does not mean that the others (0.80 nm) are converged :)) On Mar 31, 2011, at 12:20 PM, Gavin Melaugh wrote: Hi Xavier Thanks for the reply. With respect to your answer of my first query. What if you had two windows practically on top of each other, but one was not supposed to be there. e.g A window with r0 of 0.80 nm and centred at 0.78 nm and a window with r0 of 0.78 nm centred at 0.78nm. Gavin XAvier Periole wrote: On Mar 31, 2011, at 11:53 AM, Gavin Melaugh wrote: Hi All I have generated several PMF curves for the one system using umbrella sampling. In the first part of the curve (barrier region) I use a high force constant with small intervals between the windows. The latter part of the curve I use a lower force constant with larger window spacing. Anyway I have a few issues that I need clarifying: 1 - Can you have too much overlap between windows? no, there no such a thing of too much overlap :)) You could even put two identical windows with same 100% overlap ... no problem. 2 - Does the distribution at each window have to centered around the desired r0? (If not does this affect the free energy?) The deviation of the distribution from the r0 is what dictates the profile. The more away from the disired r0 the higher the free energy of the system. 3- If you over sample one particular window, will it affect the curve? There is no such a thing of over sampling ... the only thing you can have is not enough sampling. Many thanks GAvin -- gmx-users mailing listgmx-users at 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-request at gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users at 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-request at 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] Umbrella Sampling
Hi Chris many thanks again for the advise. I have, or at least I thought have sampled my barrier region to death, but as I say some histograms may not be centred around r0. I will proceed with what you suggest. Please find attached a picture of the histograms, the corresponding profile, and a sample mdp file that I use. groprofile.agr.gz Description: GNU Zip compressed data hist.agr.gz Description: GNU Zip compressed data -- 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] Umbrella sampling
Here is also the sample .mdp file chris.ne...@utoronto.ca wrote: can you show us your mdp and the pmf and the histograms for the data that you put into wham? It's a lot easier to diagnose with the real data. In the general case where umbrellas are spaced equally along your reaction coordinate, sampling overlap between umbrellas will always decrease anywhere the PMF is concave down, such as your barrier region. I would suggest adding windows at every 0.005 nm spanning the region that you consider to have a sampling problem (e.g. 0.76 to 0.83 ?) and use a much stronger force constant here (e.g. 2-3 times as strong as you used for umbrellas with 0.02 nm spacing). You have identified a problem, so my suggestion is to not bother fiddling with adding one extra replica but sample that region to death with strong force constants. I presume that this will not impact your overall efficiency too much if the reaction coordinate is long overall. Finally, you will need to evaluate the convergence of your PMF overall and perhaps of this region in particular, especially if you want to know the dG to cross it or between two low energy states on either side of it. Chris. -- original message -- Sorry I am not sure that I follow. Will the window with r0 =0.80 giving the distribution centred around 0.78nm not drive my free energy profile up. If I remove this window prior to running g_wham the free energy goes down. Should I increase the force constant so that the mean of the window is 0.80nm (bearing in mind that this is near the barrier region). Gavin XAvier Periole wrote: You can present the data differently: you have two windows at 0.78 nm giving different distribution. That indicates these windows are not converged. Does not mean that the others (0.80 nm) are converged :)) On Mar 31, 2011, at 12:20 PM, Gavin Melaugh wrote: Hi Xavier Thanks for the reply. With respect to your answer of my first query. What if you had two windows practically on top of each other, but one was not supposed to be there. e.g A window with r0 of 0.80 nm and centred at 0.78 nm and a window with r0 of 0.78 nm centred at 0.78nm. Gavin XAvier Periole wrote: On Mar 31, 2011, at 11:53 AM, Gavin Melaugh wrote: Hi All I have generated several PMF curves for the one system using umbrella sampling. In the first part of the curve (barrier region) I use a high force constant with small intervals between the windows. The latter part of the curve I use a lower force constant with larger window spacing. Anyway I have a few issues that I need clarifying: 1 - Can you have too much overlap between windows? no, there no such a thing of too much overlap :)) You could even put two identical windows with same 100% overlap ... no problem. 2 - Does the distribution at each window have to centered around the desired r0? (If not does this affect the free energy?) The deviation of the distribution from the r0 is what dictates the profile. The more away from the disired r0 the higher the free energy of the system. 3- If you over sample one particular window, will it affect the curve? There is no such a thing of over sampling ... the only thing you can have is not enough sampling. Many thanks GAvin -- gmx-users mailing listgmx-users at 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-request at gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users at 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-request at gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists umbrella114.mdp Description: application/mdp -- 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] Umbrella Sampling
looks fine to me, no need to do that extra sampling that I suggested since it appears that you already did this -- benefits of seeing real data ;). If you want to understand why your histograms are not always centered at r0 (note that this is just fine) then you should read more about US, WHAM, and how to bias/debias the data for US (I am sure that there are textbooks around that explain this). The only case in which all of your histograms will be centered at their respective r0 is when the underlying PMF is exactly flat. Chris. -- original message -- Hi Chris many thanks again for the advise. I have, or at least I thought have sampled my barrier region to death, but as I say some histograms may not be centred around r0. I will proceed with what you suggest. Please find attached a picture of the histograms, the corresponding profile, and a sample mdp file that I use. -- next part -- A non-text attachment was scrubbed... Name: groprofile.agr.gz Type: application/x-gzip Size: 3805 bytes Desc: not available Url : http://lists.gromacs.org/pipermail/gmx-users/attachments/20110331/2a5b0bd6/groprofile.agr.gz -- next part -- A non-text attachment was scrubbed... Name: hist.agr.gz Type: application/x-gzip Size: 25250 bytes Desc: not available Url : http://lists.gromacs.org/pipermail/gmx-users/attachments/20110331/2a5b0bd6/hist.agr.gz -- -- 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] Umbrella Sampling
Cheers Chris If I remove the red histogram (the first of the wider distributions), which should be centred around 0.80nm but is actually centred around 0.78 nm; and add in some more histograms with higher force constants the profile changes slightly. It seems that g_wham is very sensitive to these subtleties. How do I know which curve is correct? I have about six such curves that differ slightly in this manner. Gavin chris.ne...@utoronto.ca wrote: looks fine to me, no need to do that extra sampling that I suggested since it appears that you already did this -- benefits of seeing real data ;). If you want to understand why your histograms are not always centered at r0 (note that this is just fine) then you should read more about US, WHAM, and how to bias/debias the data for US (I am sure that there are textbooks around that explain this). The only case in which all of your histograms will be centered at their respective r0 is when the underlying PMF is exactly flat. Chris. -- original message -- Hi Chris many thanks again for the advise. I have, or at least I thought have sampled my barrier region to death, but as I say some histograms may not be centred around r0. I will proceed with what you suggest. Please find attached a picture of the histograms, the corresponding profile, and a sample mdp file that I use. -- next part -- A non-text attachment was scrubbed... Name: groprofile.agr.gz Type: application/x-gzip Size: 3805 bytes Desc: not available Url : http://lists.gromacs.org/pipermail/gmx-users/attachments/20110331/2a5b0bd6/groprofile.agr.gz -- next part -- A non-text attachment was scrubbed... Name: hist.agr.gz Type: application/x-gzip Size: 25250 bytes Desc: not available Url : http://lists.gromacs.org/pipermail/gmx-users/attachments/20110331/2a5b0bd6/hist.agr.gz -- modifiedhist.xvg.gz Description: GNU Zip compressed data modified.agr.gz Description: GNU Zip compressed data -- 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] Heat of vap
in your mail: On 30 March 2011 15:30, Justin A. Lemkul jalem...@vt.edu wrote: Elisabeth wrote: Dear all, I intend to obtain vaporization heat per volume for a /pure alkane system/. Here is the steps I am taking. Please correct me. 1- Obtain total energy of system (kinetic+potential) and divide by number of molecules to obtain energy per mol of molecules. g_energy -f *.edr -nmol XXX 2- Obtain total energy of a single molecule (use pbc). 3- Subtract step 2 from step 1. 4- Divide by simulation box volume. My questions is: in step 2 : what should be the box size? The same size as in 1 or it does not matter? (step 1 is done for the actual denstiy) More troubling, how does one define the energy of a molecule? If you use any sort of long-range algorithms (especially PME, but also dispersion correction), you can't simply decompose the system like this. Thanks Justin and David. I have been trying to find the article in which this has been presented. If you have time Please see page 5937, right column, equation 11. I think I made a mistake and I dont have to include kinetic energy, Only nonboded energies!? http://pubs.acs.org/doi/pdfplus/10.1021/jp0707539 In the derivation of recent Gromos96 parameter sets, the heat of vaporization is quite simple: DHvap = Ugas - Uliq + RT 1- So Uliq is the total energy or only potential (no kinetic) 2- How can I compute Ugas? I have liquid now... Thank you, Regards, -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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 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] Heat of vap
Elisabeth wrote: in your mail: On 30 March 2011 15:30, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Elisabeth wrote: Dear all, I intend to obtain vaporization heat per volume for a /pure alkane system/. Here is the steps I am taking. Please correct me. 1- Obtain total energy of system (kinetic+potential) and divide by number of molecules to obtain energy per mol of molecules. g_energy -f *.edr -nmol XXX 2- Obtain total energy of a single molecule (use pbc). 3- Subtract step 2 from step 1. 4- Divide by simulation box volume. My questions is: in step 2 : what should be the box size? The same size as in 1 or it does not matter? (step 1 is done for the actual denstiy) More troubling, how does one define the energy of a molecule? If you use any sort of long-range algorithms (especially PME, but also dispersion correction), you can't simply decompose the system like this. Thanks Justin and David. I have been trying to find the article in which this has been presented. If you have time Please see page 5937, right column, equation 11. I think I made a mistake and I dont have to include kinetic energy, Only nonboded energies!? http://pubs.acs.org/doi/pdfplus/10.1021/jp0707539 What is cohesive energy and how does it relate to the quantity you're trying to calculate? In the derivation of recent Gromos96 parameter sets, the heat of vaporization is quite simple: DHvap = Ugas - Uliq + RT 1- So Uliq is the total energy or only potential (no kinetic) Potential. 2- How can I compute Ugas? I have liquid now... Run a simulation in the gas phase. -Justin Thank you, Regards, -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org mailto: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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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] Heat of vap
On 2011-03-31 18.52, Elisabeth wrote: in your mail: On 30 March 2011 15:30, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Elisabeth wrote: Dear all, I intend to obtain vaporization heat per volume for a /pure alkane system/. Here is the steps I am taking. Please correct me. 1- Obtain total energy of system (kinetic+potential) and divide by number of molecules to obtain energy per mol of molecules. g_energy -f *.edr -nmol XXX 2- Obtain total energy of a single molecule (use pbc). 3- Subtract step 2 from step 1. 4- Divide by simulation box volume. My questions is: in step 2 : what should be the box size? The same size as in 1 or it does not matter? (step 1 is done for the actual denstiy) More troubling, how does one define the energy of a molecule? If you use any sort of long-range algorithms (especially PME, but also dispersion correction), you can't simply decompose the system like this. Thanks Justin and David. I have been trying to find the article in which this has been presented. If you have time Please see page 5937, right column, equation 11. I think I made a mistake and I dont have to include kinetic energy, Only nonboded energies!? Either Epot or Etot. It does not matter if you simulate at the same Temp. You could also consider using the enthalphy (gmx 4.5 and higher). http://pubs.acs.org/doi/pdfplus/10.1021/jp0707539 In the derivation of recent Gromos96 parameter sets, the heat of vaporization is quite simple: DHvap = Ugas - Uliq + RT 1- So Uliq is the total energy or only potential (no kinetic) 2- How can I compute Ugas? I have liquid now... Thank you, Regards, -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing list gmx-users@gromacs.org mailto: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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- 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/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] adding a new residue in the ff
Hi folks, I have a problem with a strange residue into a PDB file. It is a cysteinesulfonic acid, in which the -SH moiety of the Cys residue is replaced by -SO3. This modified residue is essential for the activity of this protein, therefore I must keep it into the protein. So, I'm trying to add this new residue to the force field (I'm planning to use the 43a1ff already modified for lipids in the past). Since I have Gromacs 4.5.3 I copied the ff directory on my local dir, then I attempted to modify the aminoacids.rtp file and other files following instructions in the section Adding a residue to a force field. In order to have some hints on OCS topology, I used PRODRG, at least to have some indication on atom, bonds and angle types, but in the .itp file obtained from PRODRG there are several data for which I don't find the corresponding element in the ffbonded.itp file. For example, I don't see any equivalent for the CB - SG - OD1 angle. Probably I should add them to the ffbonded.itp file, but I'm unsure how to do it. Is there an order to follow, or can I simply add a new element at the end of the [ angle ] section? Can anyone give me some hint to do it correctly, and more generally to manage correctly the whole problem? Thanks a lot Anna Marabotti __ Anna Marabotti, Ph.D. Laboratory of Bioinformatics and Computational Biology Institute of Food Science - CNR Via Roma, 64 83100 Avellino Phone: +39 0825 299651 Fax: +39 0825 781585 E-mail: amarabo...@isa.cnr.it Skype account: annam1972 Web site: http://bioinformatica.isa.cnr.it/anna/anna.htm When a man with a gun meets a man with a pen, the man with the gun is a dead man (Roberto Benigni, about Roberto Saviano) -- 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] Heat of vap
On 31 March 2011 12:58, Justin A. Lemkul jalem...@vt.edu wrote: Elisabeth wrote: in your mail: On 30 March 2011 15:30, Justin A. Lemkul jalem...@vt.edu mailto: jalem...@vt.edu wrote: Elisabeth wrote: Dear all, I intend to obtain vaporization heat per volume for a /pure alkane system/. Here is the steps I am taking. Please correct me. 1- Obtain total energy of system (kinetic+potential) and divide by number of molecules to obtain energy per mol of molecules. g_energy -f *.edr -nmol XXX 2- Obtain total energy of a single molecule (use pbc). 3- Subtract step 2 from step 1. 4- Divide by simulation box volume. My questions is: in step 2 : what should be the box size? The same size as in 1 or it does not matter? (step 1 is done for the actual denstiy) More troubling, how does one define the energy of a molecule? If you use any sort of long-range algorithms (especially PME, but also dispersion correction), you can't simply decompose the system like this. Thanks Justin and David. I have been trying to find the article in which this has been presented. If you have time Please see page 5937, right column, equation 11. I think I made a mistake and I dont have to include kinetic energy, Only nonboded energies!? http://pubs.acs.org/doi/pdfplus/10.1021/jp0707539 What is cohesive energy and how does it relate to the quantity you're trying to calculate? It is delta Hvap/volume. It is directly related to Hvap. What is happening is that they are calculating nonbonded energy of some chains, divide by number of chains and substract from nonbonded energy of a single chain in vacuum. These are the steps I wrote in my first post but I think I should not have included kinetic and should just look at LJ-SR and Coulomb-SR. I am using PME..If I remember correctly LR is included in Coulomb-SR and can not get decomposed? But I dont think this doesnt matter since if I am to take nonbonded energies this should not hurt,,, Please comment ... In the derivation of recent Gromos96 parameter sets, the heat of vaporization is quite simple: DHvap = Ugas - Uliq + RT 1- So Uliq is the total energy or only potential (no kinetic) Potential. 2- How can I compute Ugas? I have liquid now... Run a simulation in the gas phase. Sorry, but how can I do this? :( I have box of molecules with density of actual liquid..How can I shift to gas phase ..I mean how many molecules I need to keep in the box.. Many thanks... -Justin Thank you, Regards, -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org mailto: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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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 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] How to compile the template.c when GMX is builded with cmake
Dear all, When GMX is builded with cmake, how to compile the template.c? I used to make the template.c by the command make -f MakefileXXX, but it can not work in version 4.5. Thanks for your suggestions. Best regards, Bert -- 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] Heat of vap
Elisabeth wrote: On 31 March 2011 12:58, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Elisabeth wrote: in your mail: On 30 March 2011 15:30, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: Elisabeth wrote: Dear all, I intend to obtain vaporization heat per volume for a /pure alkane system/. Here is the steps I am taking. Please correct me. 1- Obtain total energy of system (kinetic+potential) and divide by number of molecules to obtain energy per mol of molecules. g_energy -f *.edr -nmol XXX 2- Obtain total energy of a single molecule (use pbc). 3- Subtract step 2 from step 1. 4- Divide by simulation box volume. My questions is: in step 2 : what should be the box size? The same size as in 1 or it does not matter? (step 1 is done for the actual denstiy) More troubling, how does one define the energy of a molecule? If you use any sort of long-range algorithms (especially PME, but also dispersion correction), you can't simply decompose the system like this. Thanks Justin and David. I have been trying to find the article in which this has been presented. If you have time Please see page 5937, right column, equation 11. I think I made a mistake and I dont have to include kinetic energy, Only nonboded energies!? http://pubs.acs.org/doi/pdfplus/10.1021/jp0707539 What is cohesive energy and how does it relate to the quantity you're trying to calculate? It is delta Hvap/volume. It is directly related to Hvap. What is happening is that they are calculating nonbonded energy of some chains, divide by number of chains and substract from nonbonded energy of a single chain in vacuum. These are the steps I wrote in my first post but I think I should not have included kinetic and should just look at LJ-SR and Coulomb-SR. I am using PME..If I remember correctly LR is included in Coulomb-SR and can not get decomposed? But I dont think this doesnt matter since if I am to take nonbonded energies this should not hurt,,, Please comment ... PME energies are from nonbonded interactions. The mesh energy is written to the Coul-recip term in the .edr file. If there is some other Coul (LR) term, it is because you're using a twin-range cutoff such that rcoulomb rlist, which I do not believe is correct when using PME. In the derivation of recent Gromos96 parameter sets, the heat of vaporization is quite simple: DHvap = Ugas - Uliq + RT 1- So Uliq is the total energy or only potential (no kinetic) Potential. 2- How can I compute Ugas? I have liquid now... Run a simulation in the gas phase. Sorry, but how can I do this? :( I have box of molecules with density of actual liquid..How can I shift to gas phase ..I mean how many molecules I need to keep in the box.. Make a box with an equivalent number of molecules separated by some large amount of space (i.e. 50 nm or so). Set pbc=no and all cutoffs to zero. I'm basing this on Gromos96 parameterization, but I don't know what your target force field is. -Justin Many thanks... -Justin Thank you, Regards, -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto: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 mailto:gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry
Re: [gmx-users] Heat of vap
On 2011-03-31 19.11, Elisabeth wrote: On 31 March 2011 12:58, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Elisabeth wrote: in your mail: On 30 March 2011 15:30, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: Elisabeth wrote: Dear all, I intend to obtain vaporization heat per volume for a /pure alkane system/. Here is the steps I am taking. Please correct me. 1- Obtain total energy of system (kinetic+potential) and divide by number of molecules to obtain energy per mol of molecules. g_energy -f *.edr -nmol XXX 2- Obtain total energy of a single molecule (use pbc). 3- Subtract step 2 from step 1. 4- Divide by simulation box volume. My questions is: in step 2 : what should be the box size? The same size as in 1 or it does not matter? (step 1 is done for the actual denstiy) More troubling, how does one define the energy of a molecule? If you use any sort of long-range algorithms (especially PME, but also dispersion correction), you can't simply decompose the system like this. Thanks Justin and David. I have been trying to find the article in which this has been presented. If you have time Please see page 5937, right column, equation 11. I think I made a mistake and I dont have to include kinetic energy, Only nonboded energies!? http://pubs.acs.org/doi/pdfplus/10.1021/jp0707539 What is cohesive energy and how does it relate to the quantity you're trying to calculate? It is delta Hvap/volume. It is directly related to Hvap. What is happening is that they are calculating nonbonded energy of some chains, divide by number of chains and substract from nonbonded energy of a single chain in vacuum. These are the steps I wrote in my first post but I think I should not have included kinetic and should just look at LJ-SR and Coulomb-SR. I am using PME..If I remember correctly LR is included in Coulomb-SR and can not get decomposed? But I dont think this doesnt matter since if I am to take nonbonded energies this should not hurt,,, Please comment ... It is simple. Compute Epot with all normal liquid options (PME, Dispcorr etc.). Compute Epot for a gas phase molecule without any cutoffs Apply equation below. For OPLS/AA we obtain close to 98% correlation between experiment and simulation (paper submitted). In the derivation of recent Gromos96 parameter sets, the heat of vaporization is quite simple: DHvap = Ugas - Uliq + RT 1- So Uliq is the total energy or only potential (no kinetic) Potential. 2- How can I compute Ugas? I have liquid now... Run a simulation in the gas phase. Sorry, but how can I do this? :( I have box of molecules with density of actual liquid..How can I shift to gas phase ..I mean how many molecules I need to keep in the box.. Many thanks... -Justin Thank you, Regards, -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto: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 mailto:gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing list gmx-users@gromacs.org
[gmx-users] Umbrella Sampling
your comment: which should be centred around 0.80nm is flawed, as i mentioned earlier. also, it is not g_wham that is sensitive but the convergence and sampling of phase space that is sensitive. don`t remove any data. do evaluate your convergence. without convergence measures, a pmf is worse than useless. chris. -- original message -- Cheers Chris If I remove the red histogram (the first of the wider distributions), which should be centred around 0.80nm but is actually centred around 0.78 nm; and add in some more histograms with higher force constants the profile changes slightly. It seems that g_wham is very sensitive to these subtleties. How do I know which curve is correct? I have about six such curves that differ slightly in this manner. Gavin chris.ne...@utoronto.ca wrote: [Hide Quoted Text] looks fine to me, no need to do that extra sampling that I suggested since it appears that you already did this -- benefits of seeing real data ;). If you want to understand why your histograms are not always centered at r0 (note that this is just fine) then you should read more about US, WHAM, and how to bias/debias the data for US (I am sure that there are textbooks around that explain this). The only case in which all of your histograms will be centered at their respective r0 is when the underlying PMF is exactly flat. Chris. -- original message -- Hi Chris many thanks again for the advise. I have, or at least I thought have sampled my barrier region to death, but as I say some histograms may not be centred around r0. I will proceed with what you suggest. Please find attached a picture of the histograms, the corresponding profile, and a sample mdp file that I use. -- 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] adding a new residue in the ff
Hi, It would probably be easier, faster, and more accurate to just use most of the parameters for Cys rather than try to have PRODRG re-create a (potentially flawed) model of your compound. The only new parameters are related to SO3, so the rest should be identical to the Cys residue. That's not a good idea. It'll only do for the backbone. The charge of CB will be quite different, as well as the CA-CB-SG angle, and for the rest there's nothing similar even. This is where parameterization becomes a chore - when there's nothing analogous to what you're doing. Proper Gromos96 parameterization methodology would dictate that you generate an analogous compound (i.e., methyl sulfonic acid) and adjust its parameters such that it reproduces various condensed-phase thermodynamic and physical properties (DeltaG of solvation, liquid density, heat of vaporization). Proper derivation is quite time-consuming. Perhaps someone has already done this work and it is published. If you're unlucky, you've got to do it all yourself. That's a good idea :) Cheers, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- 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] adding a new residue in the ff
Tsjerk Wassenaar wrote: Hi, It would probably be easier, faster, and more accurate to just use most of the parameters for Cys rather than try to have PRODRG re-create a (potentially flawed) model of your compound. The only new parameters are related to SO3, so the rest should be identical to the Cys residue. That's not a good idea. It'll only do for the backbone. The charge of CB will be quite different, as well as the CA-CB-SG angle, and for the rest there's nothing similar even. Gah, that's what I meant. Thanks for pointing that out! I guess I've stated so many times (and published on the fact) that PRODRG charges are useless that I'm no longer even quoting myself... -Justin This is where parameterization becomes a chore - when there's nothing analogous to what you're doing. Proper Gromos96 parameterization methodology would dictate that you generate an analogous compound (i.e., methyl sulfonic acid) and adjust its parameters such that it reproduces various condensed-phase thermodynamic and physical properties (DeltaG of solvation, liquid density, heat of vaporization). Proper derivation is quite time-consuming. Perhaps someone has already done this work and it is published. If you're unlucky, you've got to do it all yourself. That's a good idea :) Cheers, Tsjerk -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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] Web site issues (Search, Redmine)
I ran into some issues with the Gromacs web site: 1. I tried to register an account on the bug tracker (http://redmine.gromacs.org/account/register). Upon entering my information, I get the odd error message Email notifications is not included in the list. Perhaps this is related to http://www.redmine.org/issues/7138 ? 2. Trying to figure out what's going on, I wanted to check the mailing list archive. Searching for redmine on http://www.gromacs.org/Support/Mailing_Lists/Search gives strange results (just a few emails that are listed dozens of times). I hope this helps to track some of these things down. Best, Lutz -- 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] implicit solvent GB force table
Hi, I have been tracking the code for implicit solvent, i.e. src/mdlib/genborn.c According to the gromacs paper on implicit solvent, J Comp Chem 31:2593, 2010, the GB force is tabulated in the X = Rij Ci Cj dimension. However, the tabulated function, which I think is stored in fr-gbtab, is only used in the function gb_bonds_tab(). I could not find the function of X applied in the calc_gb_chainrule() function. Does the gbtab applied on dvda and dadx elsewhere? Thanks in advance! regards, Chi-cheng -- 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] Spatially Varying External Force
Hello, Is there a way we can apply a spatially varying external force in GROMACS. I went through the manual if anything like this is possible but couldn't find anything. Any help is appreciated. Apoorv -- 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] implicit solvent GB force table
Hi! The tabulated function is applied to all interactions, both bonded and non-bonded. The function is initialized in make_gb_table(), and accessed in the non-bonded kernels the same way as other tabulated functions are accessed. See GBtab[nnn] in the kernels for more details. In calc_gb_chainrule() the values of dadx (the derivative of the radii wrt. to the coordinates), and dvda (the derivative of the potential wrt. to the radii), which are calculated in the kernels, are simply multiplied together to yield the total force. Cheers /Per 31 mar 2011 kl. 21.09 skrev Chi-cheng Chiu: Hi, I have been tracking the code for implicit solvent, i.e. src/mdlib/genborn.c According to the gromacs paper on implicit solvent, J Comp Chem 31:2593, 2010, the GB force is tabulated in the X = Rij Ci Cj dimension. However, the tabulated function, which I think is stored in fr-gbtab, is only used in the function gb_bonds_tab(). I could not find the function of X applied in the calc_gb_chainrule() function. Does the gbtab applied on dvda and dadx elsewhere? Thanks in advance! regards, Chi-cheng -- 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 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] couple-moltype for two molecules
Dear all, I tried to use couple-moltype=Protein Ligand directive to annihilate both protein and ligand molecules using free energy method. I realized that couple-moltype key works for only one molecule type. Is it right? To perform the same annihilation I used couple-moltype=Protein to annihilate the protein and dual topology formalism (definied in itp file) to annihilate the ligand. Are these commands able to work together? Thanks Luca -- 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] Web site issues (Search, Redmine)
Hi Lutz, On 3/31/11 9:06 PM, Lutz Maibaum wrote: I ran into some issues with the Gromacs web site: 1. I tried to register an account on the bug tracker (http://redmine.gromacs.org/account/register). Upon entering my information, I get the odd error message Email notifications is not included in the list. Perhaps this is related to http://www.redmine.org/issues/7138 ? I moved the server a few days ago and haven't done one of the migration steps. Could you check again and let me know (offline is OK) if it doesn't work? 2. Trying to figure out what's going on, I wanted to check the mailing list archive. Searching for redmine on http://www.gromacs.org/Support/Mailing_Lists/Search gives strange results (just a few emails that are listed dozens of times). That's strange indeed, will fix it. I hope this helps to track some of these things down. Thanks a lot for reporting! Cheers, Rossen Best, Lutz -- 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] Taking difference of forces in two trajectories
Hi I want to test two test potentials compared to reference potential. I have md trajectories from reference potential. So I do mdrun -rerun with two different test potentials and get two separate trajectory files. Now I want to compute difference between forces acting on each atom in each frame due to different test potentials. Is there any way where two trajectories with same position values but different forces can be used to get third .trr file with forces which are difference of first two? thanks sikandar -- 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] Taking difference of forces in two trajectories
Sikandar Mashayak wrote: Hi I want to test two test potentials compared to reference potential. I have md trajectories from reference potential. So I do mdrun -rerun with two different test potentials and get two separate trajectory files. Now I want to compute difference between forces acting on each atom in each frame due to different test potentials. Is there any way where two trajectories with same position values but different forces can be used to get third .trr file with forces which are difference of first two? I don't think you can make mdrun calculate differences in two existing trajectories, but you can extract forces using g_traj and take the difference between the two output files. The file sizes may get extremely large for either long trajectories or many atoms. -Justin thanks sikandar -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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] Taking difference of forces in two trajectories
hey thanks for the explanation.. for some constraints I need to have the difference of forces in the .trr format so that I have position,velocity and force error values in one single .trr file. , I dont think g_traj would help me getting that.. is there any other option? On Thu, Mar 31, 2011 at 4:44 PM, Justin A. Lemkul jalem...@vt.edu wrote: Sikandar Mashayak wrote: Hi I want to test two test potentials compared to reference potential. I have md trajectories from reference potential. So I do mdrun -rerun with two different test potentials and get two separate trajectory files. Now I want to compute difference between forces acting on each atom in each frame due to different test potentials. Is there any way where two trajectories with same position values but different forces can be used to get third .trr file with forces which are difference of first two? I don't think you can make mdrun calculate differences in two existing trajectories, but you can extract forces using g_traj and take the difference between the two output files. The file sizes may get extremely large for either long trajectories or many atoms. -Justin thanks sikandar -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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 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] Taking difference of forces in two trajectories
Sikandar Mashayak wrote: hey thanks for the explanation.. for some constraints I need to have the difference of forces in the .trr format so that I have position,velocity and force error values in one single .trr file. , I dont think g_traj would help me getting that.. is there any other option? I don't think there is currently any tool that can do this. With the xdrfile library, though, you might be able to write your own program that can do it. -Justin On Thu, Mar 31, 2011 at 4:44 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Sikandar Mashayak wrote: Hi I want to test two test potentials compared to reference potential. I have md trajectories from reference potential. So I do mdrun -rerun with two different test potentials and get two separate trajectory files. Now I want to compute difference between forces acting on each atom in each frame due to different test potentials. Is there any way where two trajectories with same position values but different forces can be used to get third .trr file with forces which are difference of first two? I don't think you can make mdrun calculate differences in two existing trajectories, but you can extract forces using g_traj and take the difference between the two output files. The file sizes may get extremely large for either long trajectories or many atoms. -Justin thanks sikandar -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 tel:%28540%29%20231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org mailto: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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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] VDW parameters: Martini Forcefield + Implicit Solvation
Greetings, I am trying to do Martini Forcefield + Implicit solvation model for a large system and I need to supply parameters for the [ implicit_genborn_params ] section. Which I have not found. The syntax is Atomtype sar st pi gbr hct Can anybody provide me a clue about where I can find these parameters? Regards Eduardo Mendez University of Calgary -- 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] VDW parameters: Martini Forcefield + Implicit Solvation
On 1/04/2011 9:29 AM, emen...@ucalgary.ca wrote: Greetings, I am trying to do Martini Forcefield + Implicit solvation model for a large system and I need to supply parameters for the [ implicit_genborn_params ] section. Which I have not found. The syntax is Atomtype sar st pi gbr hct Can anybody provide me a clue about where I can find these parameters? Manual section 5.3.5 describes the parameters. 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
[gmx-users] RE: VDW parameters: Martini Forcefield + Implicit Solvation
Thanks for your promt reply Mark. Of course I know what is the format, that is implied in my question what I would like to know is if anybody has the specific parameters for the amber forcefield. I will try using the gbr parameters from the sigma in the LJ potentials, but I am not sure about the proper hct (or the other numbers) hence I am inquiring about this, Cheers. Eduardo Mendez Greetings, I am trying to do Martini Forcefield + Implicit solvation model for a large system and I need to supply parameters for the [ implicit_genborn_params ] section. Which I have not found. The syntax is Atomtype sar st pi gbr hct Can anybody provide me a clue about where I can find these parameters? -- 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] Installtion of gromacs-4.5.3
Hi... I am try to istalling gromacs -4.5.3 on AMD phenom II. I am following the installtions protocols, 1 St i have installed the fftw3.2.2, ./configure --enable-threads --enables-floats --enables-sse make make install then I am doing the cmake. cd gromacs-4.5.3 mkdir exec cd exec cmake ../ After cmake the make -j 6 gives me an error Linking C shared library libmd.so /usr/bin/ld: /usr/local/lib/libfftw3f.a(tensor.o): relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC /usr/local/lib/libfftw3f.a: could not read symbols: Bad value collect2: ld returned 1 exit status make[2]: *** [src/mdlib/libmd.so.6] Error 1 make[1]: *** [src/mdlib/CMakeFiles/md.dir/all] Error 2 make: *** [all] Error 2 please suggest me what I should do next... with regards Parichita Mazumder Research Fellow C/O Dr. Chaitali Mukhopadhayay Department of Chemistry University of Calcutta 92,A P C Road Kolkata-79 India.-- 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] VDW parameters: Martini Forcefield + Implicit Solvation
I meant to say, the MARTINI parameters, regards E -- 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] Installtion of gromacs-4.5.3
Hi, this question has been answered often. Please check the archive before posting. Roland On Thu, Mar 31, 2011 at 8:01 PM, parichita parichita parichitamajum...@yahoo.co.in wrote: Hi... I am try to istalling gromacs -4.5.3 on AMD phenom II. I am following the installtions protocols, 1 St i have installed the fftw3.2.2, ./configure --enable-threads --enables-floats --enables-sse make make install then I am doing the cmake. cd gromacs-4.5.3 mkdir exec cd exec cmake ../ After cmake the make -j 6 gives me an error Linking C shared library libmd.so /usr/bin/ld: /usr/local/lib/libfftw3f.a(tensor.o): relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC /usr/local/lib/libfftw3f.a: could not read symbols: Bad value collect2: ld returned 1 exit status make[2]: *** [src/mdlib/libmd.so.6] Error 1 make[1]: *** [src/mdlib/CMakeFiles/md.dir/all] Error 2 make: *** [all] Error 2 please suggest me what I should do next... with regards Parichita Mazumder Research Fellow C/O Dr. Chaitali Mukhopadhayay Department of Chemistry University of Calcutta 92,A P C Road Kolkata-79 India. -- 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 -- ORNL/UT Center for Molecular Biophysics cmb.ornl.gov 865-241-1537, ORNL PO BOX 2008 MS6309 -- 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] dipole moment of a charged peptide
Hi, I have a long-chain peptide which has a net charge of +5 . I was wondering whether the g_dipole will give any reasonable dipole moment for a molecule with a net charge. Is there any suggestion I should follow regarding calculation of dipole-moment of a charged molecule . I found that in the manual it is mentioned that 'For molecules with a net charge, the net charge is subtracted atcenter of mass of the molecule.'. I did not understand what it means. I am using gromacs-4.0.7. Sanku -- 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] Groups in mdp file
Hi, This is regarding the energygroups that one can use in the mdp file for tracking energy. Are these the groups defined in the index file? I want to know if I can define a subset of atoms in the index file and track its energy. Pooja -- Quaerendo Invenietis-Seek and you shall discover. -- 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] Installtion of gromacs-4.5.3
On 1/04/2011 11:01 AM, parichita parichita wrote: Hi... I am try to istalling gromacs -4.5.3 on AMD phenom II. I am following the installtions protocols, 1 St i have installed the fftw3.2.2, ./configure --enable-threads --enables-floats --enables-sse That's not how you successfully configured FFTW. Two of your flags do not work, for three separate uses of wrong words. make make install then I am doing the cmake. cd gromacs-4.5.3 mkdir exec cd exec cmake ../ After cmake the make -j 6 gives me an error Linking C shared library libmd.so /usr/bin/ld: /usr/local/lib/libfftw3f.a(tensor.o): relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC I have updated the http://www.gromacs.org/Downloads/Installation_Instructions to cover this issue. Mark /usr/local/lib/libfftw3f.a: could not read symbols: Bad value collect2: ld returned 1 exit status make[2]: *** [src/mdlib/libmd.so.6] Error 1 make[1]: *** [src/mdlib/CMakeFiles/md.dir/all] Error 2 make: *** [all] Error 2 please suggest me what I should do next... with regards Parichita Mazumder Research Fellow C/O Dr. Chaitali Mukhopadhayay Department of Chemistry University of Calcutta 92,A P C Road Kolkata-79 India. -- 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] Groups in mdp file
On 1/04/2011 1:30 PM, Sai Pooja wrote: Hi, This is regarding the energygroups that one can use in the mdp file for tracking energy. Are these the groups defined in the index file? Yes, the groups are defined there (or created by default if an index file is not supplied) and specified as energy groups in the .mdp file. I want to know if I can define a subset of atoms in the index file and track its energy. Yes. Whether it means anything is another matter. 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] RE: VDW parameters: Martini Forcefield + Implicit Solvation
On 1/04/2011 10:57 AM, emen...@ucalgary.ca wrote: Thanks for your promt reply Mark. Of course I know what is the format, that is implied in my question Leaving things to implication is risky. People do misunderstand, unfortunately. Fault in such cases varies :-) If what you actually want is gbr and hct parameters for Martini atom types, everyone can use their time better if you ask specifically about that. what I would like to know is if anybody has the specific parameters for the amber forcefield. I will try using the gbr parameters from the sigma in the LJ potentials, but I am not sure about the proper hct (or the other numbers) hence I am inquiring about this, That manual section mentions the reference sources for these parameters, which is why I referred to it. Whether there's any established procedure for implicit solvation with Martini is probably a question for literature search and speaking with the Martini developers. Mark Cheers. Eduardo Mendez Greetings, I am trying to do Martini Forcefield + Implicit solvation model for a large system and I need to supply parameters for the [ implicit_genborn_params ] section. Which I have not found. The syntax is Atomtype sar st pi gbr hct Can anybody provide me a clue about where I can find these parameters? -- 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] Groups in mdp file
On Thu, Mar 31, 2011 at 10:41 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 1/04/2011 1:30 PM, Sai Pooja wrote: Hi, This is regarding the energygroups that one can use in the mdp file for tracking energy. Are these the groups defined in the index file? Yes, the groups are defined there (or created by default if an index file is not supplied) and specified as energy groups in the .mdp file. I want to know if I can define a subset of atoms in the index file and track its energy. Yes. Whether it means anything is another matter. Well the idea is to modify the hamiltonian for only a subset of atoms and apply hamiltonian replica exchange. I was hoping defining energy group could be a good way to apply this(obv it would requires other changes too). 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 -- Quaerendo Invenietis-Seek and you shall discover. -- 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] Groups in mdp file
On 1/04/2011 2:06 PM, Sai Pooja wrote: On Thu, Mar 31, 2011 at 10:41 PM, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote: On 1/04/2011 1:30 PM, Sai Pooja wrote: Hi, This is regarding the energygroups that one can use in the mdp file for tracking energy. Are these the groups defined in the index file? Yes, the groups are defined there (or created by default if an index file is not supplied) and specified as energy groups in the .mdp file. I want to know if I can define a subset of atoms in the index file and track its energy. Yes. Whether it means anything is another matter. Well the idea is to modify the hamiltonian for only a subset of atoms and apply hamiltonian replica exchange. I was hoping defining energy group could be a good way to apply this(obv it would requires other changes too). Describing the overall objective is usually a good idea. Sometimes one's candidate for a solution is not best and someone else knows it :-) Here, energy groups are the only reasonable solution. 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
