Re: [gmx-users] local pressure calcuation for Gromacs-4.5
Dear all, I have made a test calculation of local pressure using version 4.5 for my membrane simulation using CHARMM FF. When rerun the simulation, mdrun gives the localpressure data. Howeve, instead of giving an anveraged data of the local pressure, mdrun gives a separate file for each frame, so I got many files: localpressure.dat0, localpressure.dat1, localpressure.dat2, localpressure.dat3 .. Then I need to calculate the pressure tensor for each frame and make average. but these localpressure.dat files are very big (each file is about 30 Mb), occupying large space of the hard disk. Can anyone give some suggestions on how to fix this? Thank you very much! The command is: mdrun_d -s lp.tpr -rerun box_md5.trr -x box_md5_rerun.xtc -o box_md5_rerun.trr -g md5_rerun.log -localpgrid 0.1 And the output message is: Dumping local pressure based on 1 frames to localpressure.dat0... Reading frame 2 time 119400.000 Dumping local pressure based on 1 frames to localpressure.dat1... Reading frame 3 time 119500.000 Dumping local pressure based on 1 frames to localpressure.dat2... Reading frame 4 time 119600.000 Dumping local pressure based on 1 frames to localpressure.dat3... Reading frame 5 time 119700.000 Dumping local pressure based on 1 frames to localpressure.dat4... Reading frame 6 time 119800.000 ... Cheers, Jianguo From: Justin A. Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Friday, 10 June 2011 07:10:35 Subject: Re: [gmx-users] local pressure calcuation for Gromacs-4.5 Amit Choubey wrote: Thanks Justin, I tried to install the recent git version but the configure file is missing. How should I install this version ? Run the bootstrap script. It generates the configure script. -Justin On Thu, Jun 9, 2011 at 12:45 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Amit Choubey wrote: Dear all, I saw an unanswered post at http://lists.gromacs.org/pipermail/gmx-users/2011-January/058063.html It is about calculating local pressure in v 4.5 when using CHARMM FF. Could someone give me some pointers about this? I don't know what the development status of version 4.5 is, but you can access it at: http://repo.or.cz/w/gromacs.git/shortlog/refs/heads/release-4-5-localpressure It hasn't been merged with release-4-5-patches in some time, so many resolved bugs won't be fixed. -Justin -- 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 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] local pressure calcuation for Gromacs-4.5
On 15/06/2011 9:09 PM, Jianguo Li wrote: Dear all, I have made a test calculation of local pressure using version 4.5 for my membrane simulation using CHARMM FF. When rerun the simulation, mdrun gives the localpressure data. Howeve, instead of giving an anveraged data of the local pressure, mdrun gives a separate file for each frame, so I got many files: localpressure.dat0, localpressure.dat1, localpressure.dat2, localpressure.dat3 .. Then I need to calculate the pressure tensor for each frame and make average. but these localpressure.dat files are very big (each file is about 30 Mb), occupying large space of the hard disk. Can anyone give some suggestions on how to fix this? Thank you very much! I would expect that the output frequency is configurable, but can only suggest you consult what documentation exists for this version. Your main alternatives are * to compress the files with (say) bzip2 or (less effective) gzip and construct a script to uncompress them singly and analyse them on the fly (AMBER users do a bit of this kind of thing, Google around) * to discard ones that are too frequent. However, judging from the numbers below, every 100ps is probably OK. Mark The command is: mdrun_d -s lp.tpr -rerun box_md5.trr -x box_md5_rerun.xtc -o box_md5_rerun.trr -g md5_rerun.log -localpgrid 0.1 And the output message is: Dumping local pressure based on 1 frames to localpressure.dat0... Reading frame 2 time 119400.000 Dumping local pressure based on 1 frames to localpressure.dat1... Reading frame 3 time 119500.000 Dumping local pressure based on 1 frames to localpressure.dat2... Reading frame 4 time 119600.000 Dumping local pressure based on 1 frames to localpressure.dat3... Reading frame 5 time 119700.000 Dumping local pressure based on 1 frames to localpressure.dat4... Reading frame 6 time 119800.000 ... Cheers, Jianguo *From:* Justin A. Lemkul jalem...@vt.edu *To:* Discussion list for GROMACS users gmx-users@gromacs.org *Sent:* Friday, 10 June 2011 07:10:35 *Subject:* Re: [gmx-users] local pressure calcuation for Gromacs-4.5 Amit Choubey wrote: Thanks Justin, I tried to install the recent git version but the configure file is missing. How should I install this version ? Run the bootstrap script. It generates the configure script. -Justin On Thu, Jun 9, 2011 at 12:45 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: Amit Choubey wrote: Dear all, I saw an unanswered post at http://lists.gromacs.org/pipermail/gmx-users/2011-January/058063.html It is about calculating local pressure in v 4.5 when using CHARMM FF. Could someone give me some pointers about this? I don't know what the development status of version 4.5 is, but you can access it at: http://repo.or.cz/w/gromacs.git/shortlog/refs/heads/release-4-5-localpressure It hasn't been merged with release-4-5-patches in some time, so many resolved bugs won't be fixed. -Justin -- 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 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 | (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 -- gmx-users mailing list
Re: [gmx-users] Questions about GB parameters
On 15/06/2011 4:24 AM, Justin A. Lemkul wrote: Hi All, I wanted to dig up an old discussion that hit the list a long time ago because I'm now encountering some problems understanding the GB settings myself. The discussion in question is here: http://lists.gromacs.org/pipermail/gmx-users/2010-August/053373.html I wanted to post a couple of questions based on Per's response. 1. Based on that post, it seems to me that the value in the gbr column should have a dielectric offset added to it during the GB calculations. In the code, though (genborn.c, around line 484 in the latest release-4-5-patches), it looks like the dielectric offset is subtracted, not added. I guess the code is reversing the process, going from GB radius back to vdW radius by subtracting the dielectric offset? It seems, then, that the parameters in gbsa.itp should specify GB radii, not vdW radii, though the manual says the gbr column is atomic van der Waals radii, which are used in computing the Born radii. Is the opposite actually true? It does look to me as though something is mis-sense here. The quantity given in gb_dielectric_offset is always subtracted from a value that I think is found in the gbr column of [implicit_genborn_parameters]. Mark 2. I am still unclear on the source of the HCT scaling factors. From the reference cited in the manual, it would seem that scaling factors are interaction-dependent, at least when H atoms are concerned. I also cannot find any indication of where these values came from. None of the values of Table 2 in the HCT reference match the contents of the hct column. Again I wonder if I'm missing something obvious :) Thanks for any insight! -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] Water Potential Energy
On 15/06/2011 4:55 AM, Rini Gupta wrote: Dear Mark, Thanks for the reply! I am using the same NPT conditions except time constants. The simulation was performed at constant temperature (300K) and pressure(1 bar) using velocity rescaling algorithm (tau=0.1 ps) for temperature coupling and Berendsen coupling scheme (tau=1 ps) for pressure coupling whereas the in the references the system was coupled to bath of constant temperature (300K) and pressure (1 bar) using time constants tau=0.4 ps for temperature coupling and taup=0.4 ps for pressure coupling. Does it is making difference in calculated and reported values? Maybe, but I'd randomly guess it would lead to a smaller difference than that. I am using LINCS algorithm to keep the geometries of all the molecules rigid. Other conditions are exactly same. To see the size effect on the system, I have also done the same calculations with 8000 molecules but result is same i.e. Water P.E=-46.7 kJ/mol. I guess that means you are observing converged quantities. Maybe they weren't observing such? There can also be differences in implementation between different codes such that absolute energies are not necessarily comparable. Energy differences should compare, however. Mark Please clarify this issue. Best Regards, Rini On Tue, 14 Jun 2011 08:13:39 +0530 wrote On 14/06/2011 4:18 AM, Rini Gupta wrote: Dear gmx-users, I am using GROMACS 4.5.4 to run a pure water system using SPC/E model containing 32000 molecules. I have done the equilibration for 2 ns followed by production run of 5 ns using NPT ensemble at 300K. I am using PME for treating electrostatic interactions (cut-off 0.9 nm). My question is Potential Energy of the system I am getting is -46.7 kJ/mol while literature value is -41.5 kJ/mol. Can anyone please tell me why this discrepancy is coming? PE is size- and method-dependent. Are you reproducing the conditions exactly? Mark -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists http://sigads.rediff.com/RealMedia/ads/click_nx.ads/www.rediffmail.com/signatureline.htm@Middle? Treat yourself at a restaurant, spa, resort and much more with *Rediff Deal ho jaye! http://track.rediff.com/click?url=___http://dealhojaye.rediff.com?sc_cid=mailsignature___cmp=signaturelnk=rediffmailsignaturenewservice=deals* -- 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] trjcat crashes with error 9360 killed when concatenating large number of frames, bug ?
I am using the command: trjcat -f *gro -o temp.xtc -cat to concatenate about 40,000 frames of 14,000 atoms each. The commands works well for 10,000 frames, but crashes for 40,000 frames after reading all the frames. There is sufficient disk space. Is this a bug of some kind? -- Maria G. Technical University of Denmark Copenhagen -- 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] trjcat crashes with error 9360 killed when concatenating large number of frames, bug ?
On 15/06/2011 10:58 PM, maria goranovic wrote: I am using the command: trjcat -f *gro -o temp.xtc -cat to concatenate about 40,000 frames of 14,000 atoms each. The commands works well for 10,000 frames, but crashes for 40,000 frames after reading all the frames. There is sufficient disk space. Is this a bug of some kind? Maybe you're running out of memory or running into a filesystem file size limit. Try doing things piece-wise. 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] trjcat crashes with error 9360 killed when concatenating large number of frames, bug ?
maria goranovic wrote: I am using the command: trjcat -f *gro -o temp.xtc -cat to concatenate about 40,000 frames of 14,000 atoms each. The commands works well for 10,000 frames, but crashes for 40,000 frames after reading all the frames. There is sufficient disk space. Is this a bug of some kind? Not a bug, but rather clunky code - trjcat consumes a huge amount of memory. If your .gro files are large, then that is the likely limitation. Convert the .gro frames to .xtc with trjconv, then concatenate those instead. -Justin -- Maria G. Technical University of Denmark Copenhagen -- 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] trjcat crashes with error 9360 killed when concatenating large number of frames, bug ?
thanks for the help .. will try On Wed, Jun 15, 2011 at 3:02 PM, Justin A. Lemkul jalem...@vt.edu wrote: maria goranovic wrote: I am using the command: trjcat -f *gro -o temp.xtc -cat to concatenate about 40,000 frames of 14,000 atoms each. The commands works well for 10,000 frames, but crashes for 40,000 frames after reading all the frames. There is sufficient disk space. Is this a bug of some kind? Not a bug, but rather clunky code - trjcat consumes a huge amount of memory. If your .gro files are large, then that is the likely limitation. Convert the .gro frames to .xtc with trjconv, then concatenate those instead. -Justin -- Maria G. Technical University of Denmark Copenhagen -- 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 -- Maria G. Technical University of Denmark Copenhagen -- 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] initial temperature ridiculously high
GZ Zhang wrote: Hi, ALL I met a bizarre in a NVT simulation in which the initial temperature is ridiculously high. Even though I specify the initial temperature to be 200 K. ; GENERATE VELOCITIES FOR STARTUP RUN gen_vel = yes gen_temp = 200.0 gen_seed = 173529 Energies (kJ/mol) Bond LJ (SR)Coulomb (SR)Coul. recip.Potential 7.17894e+013.25101e+05 -3.75274e+05 - 3.13877e+05 -3.63978e+05 Kinetic En.Total EnergyTemperature Pressure (bar) 7.97000e+04 -2.84278e+05 1.7e+04 2.75198e+06 The force field I used is called CLAYFF(http://www.sklogwiki.org/SklogWiki/index.php/CLAYFF_force_field), in which all atoms except hydroxyl groups interact through non-bonded vdW and electrostatic interactions. What's more strange is that after 5 ps, the system converted from a ordered layer structure into a disordered structure, like melting, although temperature goes to 200 K. Any comments? The combination of high temperature and really high pressure (beyond the normal +/- 1000 fluctuations) suggests that you have an unreasonable starting structure and/or broken topology. Atomic overlap (or bad parameters) will cause atoms to shoot wildly across the system, leading to large velocities and high temperature. In this case, you were fortunate that the whole system didn't explode but somehow continued. -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] Regarding H-bond autocorrelation
Thanks Sir,for your reply... I have a silly question regarding the g_hbond's autocorrelation output: The output contains the following four columns (i) Ac fin sys(t) (ii) Ac(t) (iii) Cc contact,hb(t) (iv) -dAc fs/dt As I understood the first column is the acf with background subtraction,and the second column is acf without background subtraction.Can you please refer some text from where I could get the details about the above mentioned output options and their importance in in H-bond dynamics. On Tue, Jun 14, 2011 at 16:53, Erik Marklund er...@xray.bmc.uu.se wrote: Could be. But, if memory serves me right, there's another dataset in the output, which shows the acf without the background subtraction. Erik 14 jun 2011 kl. 12.10 skrev bipin singh: I am using the Gromacs 4.5.3is that feature is present in this version.. On Mon, Jun 13, 2011 at 21:39, Erik Marklund er...@xray.bmc.uu.se wrote: Hi, The problem is that g_hbond subtracts a background level to compensate for the finite size of the system. I thought that feature had been taken away, however. Are you using old code? Erik 12 jun 2011 kl. 19.33 skrev bipin singh: Hello, I am calculating the H-bond autocorrelation using g_hbond for my system, but after plotting I have observed that the value for c(t) is reaching to negative, as far as I know it can not be negative as the probability can not be negative...please suggest where is the problem.. -- --- Thanks and Regards, Bipin Singh -- 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 --- Erik Marklund, PhD student Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: +46 18 471 4537 fax: +46 18 511 755 er...@xray.bmc.uu.se http://www2.icm.uu.se/molbio/elflab/index.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! 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 -- --- Regards, Bipin Singh -- 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 --- Erik Marklund, PhD student Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: +46 18 471 4537 fax: +46 18 511 755 er...@xray.bmc.uu.se http://www2.icm.uu.se/molbio/elflab/index.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! 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 -- --- Regards, Bipin Singh -- 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] Reducing density using -vdwd option for a new solvent in the system
Hello Justin and everybody, I created a system of charged polyhistdine, counter anions and just 1 DHB molecule is a box without making any change in the vdwradii.dat file. This system does not energy minimize, it stops with the same message: Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax 10 Double precision normally gives you higher accuracy. What can be done to fix this problem? The part of DHB itp file is: [ moleculetype ] ; Name nrexcl DHB 3 [ atoms ] ; nr type resnr resid atom cgnr charge mass 1OM 1 DHB OAA 1 -0.567 15.9994 2 C 1 DHB CAH 11.135 12.0110 3OM 1 DHB OAD 1 -0.568 15.9994 4 C 1 DHB CAK 2 -0.004 12.0110 5 CR1 1 DHB CAG 20.004 12.0110 6HC 1 DHB HAG 20.033 1.0080 7 C 1 DHB CAI 20.141 12.0110 8OA 1 DHB OAB 2 -0.179 15.9994 9 H 1 DHB HAB 20.005 1.0080 10 CR1 1 DHB CAE 30.000 12.0110 11HC 1 DHB HAE 30.000 1.0080 12 CR1 1 DHB CAF 30.000 12.0110 13HC 1 DHB HAF 30.000 1.0080 14 C 1 DHB CAJ 40.082 12.0110 15OA 1 DHB OAC 4 -0.113 15.9994 16 H 1 DHB HAC 40.031 1.0080 If I have the water/methanol or water:methanol in the system as the solvent, the system runs fine. Please help. Thanks, SN On Tue, Jun 14, 2011 at 3:13 PM, Justin A. Lemkul jalem...@vt.edu wrote: shivangi nangia wrote: Dear Justin, I have run into another problem. I created the system by including DHB in vwdradii.dat as follows: ; Very approximate VanderWaals radii ; only used for drawing atoms as balls or for calculating atomic overlap. ; longest matches are used ; '???' or '*' matches any residue name ; 'AAA' matches any protein residue name ??? C 0.15 ??? F 0.12 ??? H 0.04 ??? N 0.110 ??? O 0.105 ??? S 0.16 *DHB C 0.5 DHB H 0.5 DHB O 0.5* ; Water charge sites SOL MW0 SOL LP0 ; Masses for vsite construction GLY MN1 0 GLY MN2 0 ALA MCB1 0 ALA MCB2 0 VAL MCG1 0 VAL MCG2 0 ILE MCG1 0 ILE MCG2 0 ILE MCD1 0 ILE MCD2 0 LEU MCD1 0 LEU MCD2 0 MET MCE1 0 MET MCE2 0 TRP MTRP1 0 TRP MTRP2 0 THR MCG1 0 THR MCG2 0 LYSH MNZ1 0 LYSH MNZ2 0 After making this change, DHB molecules were not over lapping with each other. I tried to energy minimized the system. minim.mdp ; minim.mdp - used as input into grompp to generate em.tpr ; Parameters describing what to do, when to stop and what to save integrator = steep ; Algorithm (steep = steepest descent minimization) ;emtol= 1000.0; Stop minimization when the maximum force 1000.0 kJ/mol/nm emstep = 0.01 ; Energy step size nsteps = 5 ; Maximum number of (minimization) steps to perform ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist = 1 ; Frequency to update the neighbor list and long range forces ns_type = grid ; Method to determine neighbor list (simple, grid) rlist= 1.0; Cut-off for making neighbor list (short range forces) coulombtype = PME; Treatment of long range electrostatic interactions rcoulomb = 1.0; Short-range electrostatic cut-off rvdw = 1.0; Short-range Van der Waals cut-off pbc = xyz ; Periodic Boundary Conditions (yes/no) constraints = none After about 6000 steps the run stops with the message: Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax 10 Double precision normally gives you higher accuracy. Steepest Descents converged to machine precision in 6012 steps, but did not reach the requested Fmax 10. Potential Energy = 1.0655116e+05 Maximum force = 1.6512177e+02 on atom 2076 Norm of force = 6.5337501e+00 The potential energy is high, but I still continued to equilibration. After NVT equilibration, NVT equilbration runs into the following error as soon it starts: Warning: 1-4 interaction between 4512 and 4516 at distance 6.148 which is larger than the 1-4 table size 2.000 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file or with user tables increase the table size /var/spool/pbs/mom_priv/jobs/1869547.lionxj.rcc.psu.edu.SC http://1869547.lionxj.rcc.psu.edu.SC: line 14: 2359 Segmentation fault mdrun -deffnm npt So, I have three questions: 1. Is the starting structure
Re: [gmx-users] Reducing density using -vdwd option for a new solvent in the system
shivangi nangia wrote: Hello Justin and everybody, I created a system of charged polyhistdine, counter anions and just 1 DHB molecule is a box without making any change in the vdwradii.dat file. This system does not energy minimize, it stops with the same message: Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax 10 Double precision normally gives you higher accuracy. What can be done to fix this problem? Take some time to search the Gromacs website and the mailing list archive. You would have undoubtedly found either this: http://www.gromacs.org/Documentation/Errors#Stepsize_too_small.2c_or_no_change_in_energy._Converged_to_machine_precision.2c_but_not_to_the_requested_precision or the hundreds of other messages that post this message, which is neither a problem, nor an error, per se. The part of DHB itp file is: [ moleculetype ] ; Name nrexcl DHB 3 [ atoms ] ; nr type resnr resid atom cgnr charge mass 1OM 1 DHB OAA 1 -0.567 15.9994 2 C 1 DHB CAH 11.135 12.0110 3OM 1 DHB OAD 1 -0.568 15.9994 4 C 1 DHB CAK 2 -0.004 12.0110 5 CR1 1 DHB CAG 20.004 12.0110 6HC 1 DHB HAG 20.033 1.0080 7 C 1 DHB CAI 20.141 12.0110 8OA 1 DHB OAB 2 -0.179 15.9994 9 H 1 DHB HAB 20.005 1.0080 10 CR1 1 DHB CAE 30.000 12.0110 11HC 1 DHB HAE 30.000 1.0080 12 CR1 1 DHB CAF 30.000 12.0110 13HC 1 DHB HAF 30.000 1.0080 14 C 1 DHB CAJ 40.082 12.0110 15OA 1 DHB OAC 4 -0.113 15.9994 16 H 1 DHB HAC 40.031 1.0080 This topology looks like complete junk. Earlier I provided you a link to PRODRG tips and told you there was an article referenced there you should read. I certainly hope you will do so. If you run a simulation with a lousy topology, you'll get lousy results. Either the system will be unstable or the results will be completely untrustworthy. If I have the water/methanol or water:methanol in the system as the solvent, the system runs fine. Well, what's the solvent in the case of the unstable system? Just because some other systems appear stable does not mean anything else will be. -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
[gmx-users] centering a bilayer at a cartesian coordinate
Dear users:
I am trying to process a trajectory so that a group of molecules has
their center of mass at a constant position in Cartesian space. I have
not been able to figure out how to do this.
The reason that I would like this is that I have conducted umbrella
sampling of a solute along the normal to a lipid bilayer and I would
like to create a movie of a false-trajectory of the immersion profile.
Such processing is also important for generating SDFs and for use with
g_density.
I expect that the problems that I am having are due to volume
fluctuations in the NPT ensemble.
The best idea that I have tried was (gromacs 4.5.3):
trjconv -center -box 10 10 15
where the original dimensions are much less that 10 10 15
But still, when I run g_traj on the processed .gro file I do not get
similar values for the COM.
In more detail:
echo 0 | trjconv -s md1.tpr -f md1_50ps_md1.part0001.xtc -o tmp.xtc -e
10 -pbc mol
# select POPC for centering and System for output and use a .tpr with pbc=no
echo -e 13\n0\n | trjconv -s empty.tpr -f tmp.xtc -box 10 10 15
-center -pbc none -o tmp2.xtc
# select POPC for coordinate output
echo 13 | g_traj -s empty.tpr -f tmp2.xtc -ox -com -nopbc
99550 4.8424 5.00025 7.49519
99600 4.79691 4.94304 7.39868
99650 4.75789 4.85189 7.41581
99700 4.74974 4.80423 7.48257
99750 5.07858 5.04788 7.51654
99800 4.99091 4.78976 7.47778
99850 5.11406 4.84656 7.48769
99900 5.09739 5.12395 7.47889
99950 5.0411 4.88659 7.52737
10 4.91271 5.07101 7.50397
For Z, the value is 7.48037+/-0.072562 (MIN=7.3 and MAX=7.8)
If I look at the frames from the min and max z values, they do clearly
differ in the placement of the bilayer along z.
###
To simplify things, I redid this while only using the phosphorous
atoms (1 per lipid) in the centering and coordinate output.
Here, Z=7.49323+/-0.0658727 (MIN=7.3 and MAX=7.7)
To verify this and since all the atoms have the same mass, I checked
it with awk:
echo 0 | trjconv -s empty.tpr -f tmp2.xtc -dump 47550 -b 4 -o look_low.gro
echo 0 | trjconv -s empty.tpr -f tmp2.xtc -dump 80750 -b 8 -o
look_high.gro
cat look_low.gro|grep P8|awk '{s+=$NF;n++} END{print s/n}'
7.39197
cat look_high.gro|grep P8|awk '{s+=$NF;n++} END{print s/n}'
7.62207
###
Finally, I rechecked with a single atom and here it worked exactly as
expected. The atoms is placed at 5 5 7.5 in every single frame.
###
Then I checked using 2 phosphorous atoms from the same (or,
separately, different) leaflets, and the result was the same:
$ tail coord.xvg
99550 5 5 7.5
99600 5 5.0005 7.5
99650 5.0005 5.0005 7.5005
99700 5 5.0005 7.5
99750 5.0005 5 7.5005
99800 5 5.0005 7.5005
99850 5 5 7.5005
99900 5.0005 5 7.5005
99950 5.0005 5 7.4995
10 5 5 7.5
Then using 3 phosphorous atoms from (containing atoms from both
leaflets), and now there is more deviation:
$ tail coord.xvg
99550 5.48833 5.30233 6.972
99600 5.48733 5.29233 6.97167
99650 5.50033 5.29567 6.93467
99700 5.52133 5.27433 6.93967
99750 5.489 5.253 6.99133
99800 5.481 5.319 6.91533
99850 5.47867 5.309 6.827
99900 5.48733 5.292 6.83133
99950 5.52767 5.276.86867
10 5.518 5.319 6.89167
(MIN=6.7 and MAX=7.1)
I originally had problems with pbc during trjconv in which the -center
option would place the bilayer at the peripheries of the unit cell in
some frames (COM should still be at the center). This is what lead me
to the route that I have used above (a .tpr that was generated with
pbc=no and trjconv -pbc none -center). Nevertheless, I think that
perhaps trjconv is using pbc information even in this case where ti
should not.
##
If anybody can see what I am doing wrong or has a method to center a
bilayer at a cartesian coordinate, then I am very interested.
Thank you for your time,
Chris.
--
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] centering a bilayer at a cartesian coordinate
I solved it. It was my own error to assume that trjconv -center
centers the COM. Actually, it centers the value of (min+max)/2 in each
dimension.
I can modify trjconv locally to do what I want.
Thank you,
Chris.
static void center_x(int ecenter,rvec x[],matrix box,int n,int
nc,atom_id ci[])
{
int i,m,ai;
rvec cmin,cmax,box_center,dx;
if (nc 0) {
copy_rvec(x[ci[0]],cmin);
copy_rvec(x[ci[0]],cmax);
for(i=0; inc; i++) {
ai=ci[i];
for(m=0; mDIM; m++) {
if (x[ai][m] cmin[m])
cmin[m]=x[ai][m];
else if (x[ai][m] cmax[m])
cmax[m]=x[ai][m];
}
}
calc_box_center(ecenter,box,box_center);
for(m=0; mDIM; m++)
dx[m] = box_center[m]-(cmin[m]+cmax[m])*0.5;
for(i=0; in; i++)
rvec_inc(x[i],dx);
}
}
Quoting chris.ne...@utoronto.ca:
Dear users:
I am trying to process a trajectory so that a group of molecules has
their center of mass at a constant position in Cartesian space. I have
not been able to figure out how to do this.
The reason that I would like this is that I have conducted umbrella
sampling of a solute along the normal to a lipid bilayer and I would
like to create a movie of a false-trajectory of the immersion profile.
Such processing is also important for generating SDFs and for use with
g_density.
I expect that the problems that I am having are due to volume
fluctuations in the NPT ensemble.
The best idea that I have tried was (gromacs 4.5.3):
trjconv -center -box 10 10 15
where the original dimensions are much less that 10 10 15
But still, when I run g_traj on the processed .gro file I do not get
similar values for the COM.
In more detail:
echo 0 | trjconv -s md1.tpr -f md1_50ps_md1.part0001.xtc -o tmp.xtc -e
10 -pbc mol
# select POPC for centering and System for output and use a .tpr with pbc=no
echo -e 13\n0\n | trjconv -s empty.tpr -f tmp.xtc -box 10 10 15
-center -pbc none -o tmp2.xtc
# select POPC for coordinate output
echo 13 | g_traj -s empty.tpr -f tmp2.xtc -ox -com -nopbc
99550 4.8424 5.00025 7.49519
99600 4.79691 4.94304 7.39868
99650 4.75789 4.85189 7.41581
99700 4.74974 4.80423 7.48257
99750 5.07858 5.04788 7.51654
99800 4.99091 4.78976 7.47778
99850 5.11406 4.84656 7.48769
99900 5.09739 5.12395 7.47889
99950 5.0411 4.88659 7.52737
104.91271 5.07101 7.50397
For Z, the value is 7.48037+/-0.072562 (MIN=7.3 and MAX=7.8)
If I look at the frames from the min and max z values, they do clearly
differ in the placement of the bilayer along z.
###
To simplify things, I redid this while only using the phosphorous
atoms (1 per lipid) in the centering and coordinate output.
Here, Z=7.49323+/-0.0658727 (MIN=7.3 and MAX=7.7)
To verify this and since all the atoms have the same mass, I checked
it with awk:
echo 0 | trjconv -s empty.tpr -f tmp2.xtc -dump 47550 -b 4 -o
look_low.gro
echo 0 | trjconv -s empty.tpr -f tmp2.xtc -dump 80750 -b 8 -o
look_high.gro
cat look_low.gro|grep P8|awk '{s+=$NF;n++} END{print s/n}'
7.39197
cat look_high.gro|grep P8|awk '{s+=$NF;n++} END{print s/n}'
7.62207
###
Finally, I rechecked with a single atom and here it worked exactly as
expected. The atoms is placed at 5 5 7.5 in every single frame.
###
Then I checked using 2 phosphorous atoms from the same (or,
separately, different) leaflets, and the result was the same:
$ tail coord.xvg
99550 5 5 7.5
99600 5 5.0005 7.5
99650 5.0005 5.0005 7.5005
99700 5 5.0005 7.5
99750 5.0005 5 7.5005
99800 5 5.0005 7.5005
99850 5 5 7.5005
99900 5.0005 5 7.5005
99950 5.0005 5 7.4995
105 5 7.5
Then using 3 phosphorous atoms from (containing atoms from both
leaflets), and now there is more deviation:
$ tail coord.xvg
99550 5.48833 5.30233 6.972
99600 5.48733 5.29233 6.97167
99650 5.50033 5.29567 6.93467
99700 5.52133 5.27433 6.93967
99750 5.489 5.253 6.99133
99800 5.481 5.319 6.91533
99850 5.47867 5.309 6.827
99900 5.48733 5.292 6.83133
99950 5.52767 5.276.86867
105.518 5.319 6.89167
(MIN=6.7 and MAX=7.1)
I originally had problems with pbc during trjconv in which the -center
option would place the bilayer at the peripheries of the unit cell in
some frames (COM should still be at the center). This is what lead me
to the route that I have used above (a .tpr that was generated with
pbc=no and trjconv -pbc none -center). Nevertheless, I think that
perhaps trjconv is using pbc information even in this case where ti
should not.
##
If anybody can see what I am doing wrong or has a method to center a
bilayer at a cartesian coordinate, then I am very interested.
Thank you for your time,
Chris.
--
gmx-users
[gmx-users] CHARMM forcefield
Hi, I have two questions about using the charmm force field. 1. Do we still need to use the two perl scripts, convert_charmm_ to_gromacs.pl and fix_top_for_charmm.pl? 2. I got the following note when I tried to do energy minim. with grompp: NOTE 1 [file topol.top]: The largest charge group contains 12 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. Is this a problem? Thanks for your insight! Simon -- 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] local pressure calcuation for Gromacs-4.5
Dear all, Could anyone direct me to the manual for local pressure calculation or a place where everything is mentioned about it ? I have been only able to collect bits and pieces from the mailing lists. Thank you Amit On Wed, Jun 15, 2011 at 5:35 AM, Mark Abraham mark.abra...@anu.edu.auwrote: On 15/06/2011 9:09 PM, Jianguo Li wrote: Dear all, I have made a test calculation of local pressure using version 4.5 for my membrane simulation using CHARMM FF. When rerun the simulation, mdrun gives the localpressure data. Howeve, instead of giving an anveraged data of the local pressure, mdrun gives a separate file for each frame, so I got many files: localpressure.dat0, localpressure.dat1, localpressure.dat2, localpressure.dat3 .. Then I need to calculate the pressure tensor for each frame and make average. but these localpressure.dat files are very big (each file is about 30 Mb), occupying large space of the hard disk. Can anyone give some suggestions on how to fix this? Thank you very much! I would expect that the output frequency is configurable, but can only suggest you consult what documentation exists for this version. Your main alternatives are * to compress the files with (say) bzip2 or (less effective) gzip and construct a script to uncompress them singly and analyse them on the fly (AMBER users do a bit of this kind of thing, Google around) * to discard ones that are too frequent. However, judging from the numbers below, every 100ps is probably OK. Mark The command is: mdrun_d -s lp.tpr -rerun box_md5.trr -x box_md5_rerun.xtc -o box_md5_rerun.trr -g md5_rerun.log -localpgrid 0.1 And the output message is: Dumping local pressure based on 1 frames to localpressure.dat0... Reading frame 2 time 119400.000 Dumping local pressure based on 1 frames to localpressure.dat1... Reading frame 3 time 119500.000 Dumping local pressure based on 1 frames to localpressure.dat2... Reading frame 4 time 119600.000 Dumping local pressure based on 1 frames to localpressure.dat3... Reading frame 5 time 119700.000 Dumping local pressure based on 1 frames to localpressure.dat4... Reading frame 6 time 119800.000 ... Cheers, Jianguo -- *From:* Justin A. Lemkul jalem...@vt.edu jalem...@vt.edu *To:* Discussion list for GROMACS users gmx-users@gromacs.orggmx-users@gromacs.org *Sent:* Friday, 10 June 2011 07:10:35 *Subject:* Re: [gmx-users] local pressure calcuation for Gromacs-4.5 Amit Choubey wrote: Thanks Justin, I tried to install the recent git version but the configure file is missing. How should I install this version ? Run the bootstrap script. It generates the configure script. -Justin On Thu, Jun 9, 2011 at 12:45 PM, Justin A. Lemkul jalem...@vt.edumailto: jalem...@vt.edu wrote: Amit Choubey wrote: Dear all, I saw an unanswered post at http://lists.gromacs.org/pipermail/gmx-users/2011-January/058063.html It is about calculating local pressure in v 4.5 when using CHARMM FF. Could someone give me some pointers about this? I don't know what the development status of version 4.5 is, but you can access it at: http://repo.or.cz/w/gromacs.git/shortlog/refs/heads/release-4-5-localpressure It hasn't been merged with release-4-5-patches in some time, so many resolved bugs won't be fixed. -Justin -- 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
Re: [gmx-users] CHARMM forcefield
simon sham wrote: Hi, I have two questions about using the charmm force field. 1. Do we still need to use the two perl scripts, convert_charmm_ to_gromacs.pl and fix_top_for_charmm.pl? No. 2. I got the following note when I tried to do energy minim. with grompp: NOTE 1 [file topol.top]: The largest charge group contains 12 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. Is this a problem? Yes. CHARMM topologies should not use charge groups. You should invoke pdb2gmx with the -nochargegrp option to create a proper topology. -Justin Thanks for your insight! Simon -- 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] local pressure calcuation for Gromacs-4.5
Amit Choubey wrote: Dear all, Could anyone direct me to the manual for local pressure calculation or a place where everything is mentioned about it ? I have been only able to collect bits and pieces from the mailing lists. That's probably all there is to be found. There's no manual linked from the git web interface or the ftp site. -Justin Thank you Amit On Wed, Jun 15, 2011 at 5:35 AM, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote: On 15/06/2011 9:09 PM, Jianguo Li wrote: Dear all, I have made a test calculation of local pressure using version 4.5 for my membrane simulation using CHARMM FF. When rerun the simulation, mdrun gives the localpressure data. Howeve, instead of giving an anveraged data of the local pressure, mdrun gives a separate file for each frame, so I got many files: localpressure.dat0, localpressure.dat1, localpressure.dat2, localpressure.dat3 .. Then I need to calculate the pressure tensor for each frame and make average. but these localpressure.dat files are very big (each file is about 30 Mb), occupying large space of the hard disk. Can anyone give some suggestions on how to fix this? Thank you very much! I would expect that the output frequency is configurable, but can only suggest you consult what documentation exists for this version. Your main alternatives are * to compress the files with (say) bzip2 or (less effective) gzip and construct a script to uncompress them singly and analyse them on the fly (AMBER users do a bit of this kind of thing, Google around) * to discard ones that are too frequent. However, judging from the numbers below, every 100ps is probably OK. Mark The command is: mdrun_d -s lp.tpr -rerun box_md5.trr -x box_md5_rerun.xtc -o box_md5_rerun.trr -g md5_rerun.log -localpgrid 0.1 And the output message is: Dumping local pressure based on 1 frames to localpressure.dat0... Reading frame 2 time 119400.000 Dumping local pressure based on 1 frames to localpressure.dat1... Reading frame 3 time 119500.000 Dumping local pressure based on 1 frames to localpressure.dat2... Reading frame 4 time 119600.000 Dumping local pressure based on 1 frames to localpressure.dat3... Reading frame 5 time 119700.000 Dumping local pressure based on 1 frames to localpressure.dat4... Reading frame 6 time 119800.000 ... Cheers, Jianguo *From:* Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu *To:* Discussion list for GROMACS users gmx-users@gromacs.org mailto:gmx-users@gromacs.org *Sent:* Friday, 10 June 2011 07:10:35 *Subject:* Re: [gmx-users] local pressure calcuation for Gromacs-4.5 Amit Choubey wrote: Thanks Justin, I tried to install the recent git version but the configure file is missing. How should I install this version ? Run the bootstrap script. It generates the configure script. -Justin On Thu, Jun 9, 2011 at 12:45 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: Amit Choubey wrote: Dear all, I saw an unanswered post at http://lists.gromacs.org/pipermail/gmx-users/2011-January/058063.html It is about calculating local pressure in v 4.5 when using CHARMM FF. Could someone give me some pointers about this? I don't know what the development status of version 4.5 is, but you can access it at: http://repo.or.cz/w/gromacs.git/shortlog/refs/heads/release-4-5-localpressure It hasn't been merged with release-4-5-patches in some time, so many resolved bugs won't be fixed. -Justin -- 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 tel:%28540%29%20231-9080 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 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
[gmx-users] Including quadrupole-charge interaction in GROMACS
Dear GMXers, Is there a way in GROMACS to include quadrupole-charge interaction? Or is there a standard to way to mimic quadrupole moment using partial charge? Thank you. Best, Yanbin -- 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] g_density
Dear Matthias: Did you run trjconv -center -pbc mol at some point before running g_density? With pbc, there are multiple ways to put the center of a system at the center of the box. This can lead to having the water slab in the center of the unit cell and the bilayer on the top and bottom z. Without seeing the commands and the output, it is hard to say any more. Chris. -- original message -- Hi, I have aligned a trajectory to a reference structure and have now run g_density on both the original and the aligned trajectory in order to find the bilayer headgroup position and the bilayer thickness. g_density works fine with the original trajectory but there seems to be a bug when running it to the aligned structure (Alignment done using trjconv -fit progressive). The density is calculated along the z direction (-d Z). The density for positive z is calculated correctly, but the density for negative z is shifted about 15nm to to the top end of the box size, as if the density distribution along the z-axis were discontinuous. Other then stitching the data together by hands, are there any obvious better solutions? Thanks, Matthias -- 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] Position restraints
Greetings all, I have run into a little bit of a problem. I am trying to simulate a hetro-dimer. Through previous work we have identified 302 C-alphas (of 960 odd residues) that don't move much. Previously we position restrained these atoms in our simulations using charmm which gave us a significant speed up in simulation time. My supervisor is keen for me to do a comparison of that method with a completely unrestrained system using the 53A6 FF. I managed to generate a position restraint file using the .gro file and genrestr. However when I get to the simulation step I can't get grompp to work. I ran genrestr -f em.gro -n subset.ndx -o subset.itp -disre -constr As I understand my situation grompp is looking for atom numbers in subset.itp and matching them to the atom numbers in topol_Protein_chain_x.itp and since the atom numbers in subset.itp are based on the em.gro file it fails/goes out of range. Thanks to some chain breaks in my structure I have 6 chains instead of 2, is there a way convert the .gro numbers into the .itp numbers? and hence generate my restraint files based on the topol_Protein_chain_x.itp files? Furthermore can I actually do a constraint matrix over multiple molecules? Or is there a better way of achieving my desired result? (302 atoms across 2 (6) chains constrained in their relative positions) All the best, Tom Fatal error: [ file subset.itp, line 145 ]: Atom index (5222) in constraints out of bounds (1-5149). This probably means that you have inserted topology section constraints in a part belonging to a different molecule than you intended to. In that case move the constraints section to the right molecule. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- My topology file ; ; File 'topol.top' was generated ; By user: onbekend (0) ; On host: onbekend ; At date: Tue May 31 11:44:23 2011 ; ; This is a standalone topology file ; ; It was generated using program: ; pdb2gmx - VERSION 4.5.3 ; ; Command line was: ; pdb2gmx -f 3LP2.pdb -o 3lp2 -ignh -v ; ; Force field was read from the standard Gromacs share directory. ; ; Include forcefield parameters #include gromos53a6.ff/forcefield.itp ; Include chain topologies #include topol_Protein_chain_A.itp #ifdef POSRES #include posre_Protein_chain_A.itp #endif #include topol_Protein_chain_A2.itp #ifdef POSRES #include posre_Protein_chain_A2.itp #endif #ifdef REST #include subset.itp #endif #include topol_Protein_chain_B.itp #ifdef POSRES #include posre_Protein_chain_B.itp #endif #ifdef REST #include subset.itp #endif #include topol_Protein_chain_B2.itp #ifdef POSRES #include posre_Protein_chain_B2.itp #endif #ifdef REST #include subset.itp #endif #include topol_Protein_chain_B3.itp #ifdef POSRES #include posre_Protein_chain_B3.itp #endif #ifdef REST #include subset.itp #endif #include topol_Protein_chain_B4.itp #ifdef POSRES #include posre_Protein_chain_B4.itp #endif #ifdef REST #include subset.itp #endif ___ -- 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
