[gmx-users] modification of LJ potential
Dear GROMACS users,I went through the mailing list but I am still not sure about my problem. I am going to simulate two chains in a tube using GROMACS. The chains are modeled as strings of connected beads and I would like to describe the interaction with the tube aligned with z axis and passing through [0,0,0] by and additional term to LJ potential in which the r=R-sqrt(x^2+y^2); R is the radius of a tube.I want to simulate this system without pbc. Could you be so kind and give me advice which files of the source code should I modify? Thank you in advance.GreetingsZuzana -- 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] dispersion corrections in an anisotropic system
Dear GROMACS users,my system is composed of a repulsive surface with chains grafted on it and other free chains above this immobilized system. I am hesitating whether to use dispersion corrections for the pressure and energy or not. Without these corrections the repulsion of the grafting surface increases which is understandable. This is however, no a problem because under such conditions I can decrease this repulsion by the manipulation of LJ parameters. However, I think that the dispersion corrections are necessary for representation of the interactions between the bulk free chains wetting the anchored chains. Though in the melt they should be screened, but I am varying the densities of the system and not all cases represent melt situation. I have checked the mailing list but I have not found satisfactory answer. I have not found some way how to treat long range interactions of heterogeneous system.My next question is very trivial, but I can not find in Manual and other sources meaning of AllEnerPres.Thank you for your answer in advance.GreetingsZuzana -- 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_hbond and 4.5.2 version
Dear Justin, maybe following information helps you. When I evaluated the number of hydrogen bonds between two different groups, particularly, water and frozen atoms of the siloxane surface I got the same results with both version of GROMACS, 4.0.3 and 4.5.2.GreetingsZuzanaOn 02/15/11, Zuzana Benkova wrote:Hello Justin, I was using cubic boxes. GreetingsZuzanaOn 02/15/11, Erik Marklund wrote:Justin A. Lemkul skrev 2011-02-09 23.03:>>>Zuzana Benkova wrote:>>Dear GROMACS users,>>>>I have used g_hbond of version 4.5.2 to analyze number of hydrogen bonds in water. I got the average number per time frame and number of water oxygen atoms equal to 0.839. When I used g_hbond of version 4.0.7 I got 1.677, which is twice the former value. TIP3P model predicts over 3 hydrogen bonds per one water molecule. I am a bit puzzled. If I multiply the digit from version 4.0.7. by 2 I get the expected number. That is why I supposed that the number of 1.677 means per one water oxygen and per one water molecule means 2x1.677 since two water molecules participate at one hydrogen bond.>>However, I do not know yet if my interpretation is correct and how to interpret the number obtained by version 4.5.2.>>I would appreciate any help. Thank you in advance.>>>>Try pulling the latest stable development version. This issue was reported in 4.5.1:>>http://lists.gromacs.org/pipermail/gmx-users/2010-October/054905.html>>but not fixed until after 4.5.3 was released:>>http://lists.gromacs.org/pipermail/gmx-users/2010-December/056406.html>>-Justin>>>Greetings>>Zuzana>>>Are people who are reporting this error using a triclinic boxes or cuboid boxes. That information may help my bugfixing.-- ---Erik Marklund, PhD studentDept. of Cell and Molecular Biology, Uppsala University.Husargatan 3, Box 596, 75124 Uppsala, Swedenphone: +46 18 471 4537 fax: +46 18 511 755er...@xray.bmc.uu.se http://folding.bmc.uu.se/-- gmx-users mailing list gmx-users@gromacs.orghttp://lists.gromacs.org/mailman/listinfo/gmx-usersPlease 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_hbond and 4.5.2 version
Hello Justin, I was using cubic boxes. GreetingsZuzanaOn 02/15/11, Erik Marklund wrote:Justin A. Lemkul skrev 2011-02-09 23.03:>>>Zuzana Benkova wrote:>>Dear GROMACS users,>>>>I have used g_hbond of version 4.5.2 to analyze number of hydrogen bonds in water. I got the average number per time frame and number of water oxygen atoms equal to 0.839. When I used g_hbond of version 4.0.7 I got 1.677, which is twice the former value. TIP3P model predicts over 3 hydrogen bonds per one water molecule. I am a bit puzzled. If I multiply the digit from version 4.0.7. by 2 I get the expected number. That is why I supposed that the number of 1.677 means per one water oxygen and per one water molecule means 2x1.677 since two water molecules participate at one hydrogen bond.>>However, I do not know yet if my interpretation is correct and how to interpret the number obtained by version 4.5.2.>>I would appreciate any help. Thank you in advance.>>>>Try pulling the latest stable development version. This issue was reported in 4.5.1:>>http://lists.gromacs.org/pipermail/gmx-users/2010-October/054905.html>>but not fixed until after 4.5.3 was released:>>http://lists.gromacs.org/pipermail/gmx-users/2010-December/056406.html>>-Justin>>>Greetings>>Zuzana>>>Are people who are reporting this error using a triclinic boxes or cuboid boxes. That information may help my bugfixing.-- ---Erik Marklund, PhD studentDept. of Cell and Molecular Biology, Uppsala University.Husargatan 3, Box 596, 75124 Uppsala, Swedenphone: +46 18 471 4537 fax: +46 18 511 755er...@xray.bmc.uu.se http://folding.bmc.uu.se/-- gmx-users mailing list gmx-users@gromacs.orghttp://lists.gromacs.org/mailman/listinfo/gmx-usersPlease 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] g_hbond and 4.5.2 version
Dear GROMACS users,I have used g_hbond of version 4.5.2 to analyze number of hydrogen bonds in water. I got the average number per time frame and number of water oxygen atoms equal to 0.839. When I used g_hbond of version 4.0.7 I got 1.677, which is twice the former value. TIP3P model predicts over 3 hydrogen bonds per one water molecule. I am a bit puzzled. If I multiply the digit from version 4.0.7. by 2 I get the expected number. That is why I supposed that the number of 1.677 means per one water oxygen and per one water molecule means 2x1.677 since two water molecules participate at one hydrogen bond. However, I do not know yet if my interpretation is correct and how to interpret the number obtained by version 4.5.2. I would appreciate any help. Thank you in advance.GreetingsZuzana -- 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] CHARMM FF and cmap
Dear GROMACS users,I would like to run some simulations of systems combined of polyethylene oxide brushes and short homooligopeptides (alanine, 12 residues) using CHARMM force field with GROAMCS 4.0.5 version. I have used parameters from the CHARMM force field files from the newest version of GROMACS. I have prepared rtp files, converted the dihedral potential from type 9 to type 3 (Ryckaert-Bellemans) in ffbonded.itp. I can not prepare topol.top file when using pdb2gms -ff ... -f ... I am geting the following error messageProgram pdb2gmx, VERSION 4.0.3Source code file: resall.c, line: 344Fatal error:in .rtp file in residue cmap at line: -C N CA C +NCan I run these simulations with including CMAP.itp in 4.0.5 version. I have tried to omit the cmap.itp in the forcefield.itp, and removed [cmap] section in rtp and thus to neglect the CMAP correction, but I still got the same message. I have checked the mailing list but have not found answer to my questions. I would be very thanful for any suggestions and adviceGreetingsZuzana -- 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] density tip3p
Hi Nisha,I did not try OPLSAA since I need TIP3P model with CHARMM. With this FF hydrogens are also considered as interaction sites. This is not very good combination for GROMACS, but it appeared that the differences are not too big and the time required for simulation with H interacttion side is significantly larger. From my experience rdf is not too sensitive to cut-offs. Try to estimate for instance dielectric constant, dipole moment, diffusion coefficient to be entirely sure. But I think you are getting equlibrated system. Good luckZuzana Dňa 04/01/10, nishap.pa...@utoronto.ca napísal:Hi Zuzana, You are right. I did get my density to ~0.986g/cm3, and I actually came across this other paper by Price and Brooks, and initially they get a density of Tip3p using pme at around 0.979g/cm3, but they tweak some of the parameters in oplsaa to get the correct density. I am not sure if you have tried that and if that helps at all, but also they are using a different simulation package.I am getting good rdf values for the water even with slightly low density, so I guess it is okay.ThanksQuoting Zuzana Benkova :>Hi Nisha,>>I have performed a benchmark simulations of TIP3P water and I still>obtained density 0.984g.cm-3. It looks that this model gives such a>density. If you look at JCP 79, 926, 1983 you will see that the>authors got 0.982g.cm-3 with MC. (Table 3) Try to evaluate alsoo>other properties, each model of water has some deficiencies. I tried>large number of cut-offs combinations LJ and QQ tyoes of>interactions, but the density did not gange by more than 0.001g.cm-3.>>>Greetings>>Zuzana>>Dňa 03/31/10, nishap.pa...@utoronto.ca napísal:Hello,>> So I looked at the manual and I changed my mdp parameters as>follows to equilibrate at a constant pressure.>> RUN CONTROL PARAMETERS =>integrator = sd>tinit = 0>dt = 0.002>nsteps = 50>nstcomm = 1>nstxout = 0>nstvout = 0>nstfout = 0>nstlog = 500>nstenergy = 500>nstxtcout = 0>xtc-precision = 1000>nstlist = 5>ns_type = grid>pbc = xyz>rlist = 1.3>coulombtype = pme>rcoulomb = 1.3>epsilon-r = 1>vdw-type = switch>rvdw-switch = 1.0>rvdw = 1.2>DispCorr = EnerPres>fourierspacing = 0.1>fourier_nx = 0>fourier_ny = 0>fourier_nz = 0>pme_order = 6>ewald_rtol = 1e-06>epsilon_surface = 0>optimize_fft = no>tc_grps = system>tau_t = 0.1>ref_t = 298>Pcoupl = berendsen>tau_p = 1.0>compressibility = 4.5e-05>ref_p = 1.0>constraints = all-bonds>constraint-algorithm = Lincs>unconstrained-start = no>lincs-order = 4>lincs-warnangle = 30>lincs-iter = 1>gen_vel = yes>gen_temp = 298.0>gen_seed = 173529>>I also tried using mdp parameters as mentioned in some of the gromacs>tutorials. I ran this simulation for 1ns and I am still getting>density around 985g/l, which is low for tip3p water (27nm^3, 900>water molecules). I checked some of the publications and the values>they obtained were ~998g/l. I checked for vacuum in my system, but I>didn't see anything out of the ordinary. Any insights?>>Thanks>>Nisha P>>Quoting nishap.pa...@utoronto.ca:>>>Thanks. I will look up the manual again.>>>>Quoting Sander Pronk :>>>>>Hi Nisha,>>>>>>Looking at your .mdp, there are some issues that might lead to the>>>behavior that you describe:>>>First: you should try to look up the published densities for tip3p>>>water at 300K - they might actually be close to what you get.>>>Second: your neighbor list cut-off (rlist) might be too small to>>>fully contain the charge groups (check the manual, section 7.3.11).>>>Third: You haven't enabled long-range mean field correction for the>>>pressure or energy. Expect the pressure to be strongly dependent on>>>cut-off (see the same section).>>>>>>Sander>>>>>>>>>On Mar 30, 2010, at 22:47 , nishap.pa...@utoronto.ca wrote:>>>>>>>I have a box (3x3x3nm) of Tip3p water molecules ~900 and the>>>>density when I create the box u
Re: [gmx-users] density tip3p
Hi Nisha,I have performed a benchmark simulations of TIP3P water and I still obtained density 0.984g.cm-3. It looks that this model gives such a density. If you look at JCP 79, 926, 1983 you will see that the authors got 0.982g.cm-3 with MC. (Table 3) Try to evaluate alsoo other properties, each model of water has some deficiencies. I tried large number of cut-offs combinations LJ and QQ tyoes of interactions, but the density did not gange by more than 0.001g.cm-3. GreetingsZuzanaDňa 03/31/10, nishap.pa...@utoronto.ca napísal:Hello, So I looked at the manual and I changed my mdp parameters as follows to equilibrate at a constant pressure. RUN CONTROL PARAMETERS =integrator = sdtinit = 0dt = 0.002nsteps = 50nstcomm = 1nstxout = 0nstvout = 0nstfout = 0nstlog = 500nstenergy = 500nstxtcout = 0xtc-precision = 1000nstlist = 5ns_type = gridpbc = xyzrlist = 1.3coulombtype = pmercoulomb = 1.3epsilon-r = 1vdw-type = switchrvdw-switch = 1.0rvdw = 1.2DispCorr = EnerPresfourierspacing = 0.1fourier_nx = 0fourier_ny = 0fourier_nz = 0pme_order = 6ewald_rtol = 1e-06epsilon_surface = 0optimize_fft = notc_grps = systemtau_t = 0.1ref_t = 298Pcoupl = berendsentau_p = 1.0compressibility = 4.5e-05ref_p = 1.0constraints = all-bondsconstraint-algorithm = Lincsunconstrained-start = nolincs-order = 4lincs-warnangle = 30lincs-iter = 1gen_vel = yesgen_temp = 298.0gen_seed = 173529I also tried using mdp parameters as mentioned in some of the gromacs tutorials. I ran this simulation for 1ns and I am still getting density around 985g/l, which is low for tip3p water (27nm^3, 900 water molecules). I checked some of the publications and the values they obtained were ~998g/l. I checked for vacuum in my system, but I didn't see anything out of the ordinary. Any insights?ThanksNisha PQuoting nishap.pa...@utoronto.ca:>Thanks. I will look up the manual again.>>Quoting Sander Pronk :>>>Hi Nisha,Looking at your .mdp, there are some issues that might lead to the>>behavior that you describe:>>First: you should try to look up the published densities for tip3p>>water at 300K - they might actually be close to what you get.>>Second: your neighbor list cut-off (rlist) might be too small to>>fully contain the charge groups (check the manual, section 7.3.11).>>Third: You haven't enabled long-range mean field correction for the>>pressure or energy. Expect the pressure to be strongly dependent on>>cut-off (see the same section).Sander>>On Mar 30, 2010, at 22:47 , nishap.pa...@utoronto.ca wrote:>I have a box (3x3x3nm) of Tip3p water molecules ~900 and the>>>density when I create the box using genbox is 997.177g/l. I did>>>energy minimization run and the potential energy did converge>>>smoothly, so I did NPT equilibration run of 100ps and I got the>>>density value of 975g/l. Why does the density decrease after the>>>run? these are the parameters that I used :>>RUN CONTROL PARAMETERS>>>integrator = md>>>tinit = 0>>>dt = 0.002>>>nsteps = 5>>>nstcomm = 0>>>nstxout = 0>>>nstvout = 0>>>nstfout = 0>>>nstlog = 100>>>nstenergy = 100>>>nstxtcout = 0>>>xtc_precision = 1000>>>nstlist = 5>>>ns-type = Grid>>>pbc = xyz>>>rlist = 1.1>>>coulombtype = pme>>>rcoulomb = 1.1>>>epsilon-r = 1>>>vdw-type = switch>>>rvdw-switch = 0.8>>>rvdw = 1.0>>>Tcoupl = V-rescale>>>tc-grps = System>>>tau_t = 0.1>>>ref_t = 300>>>Pcoupl = berendsen>>>tau_p = 0.5>>>compressibility = 4e-05>>>ref_p = 1.0>>>constraints = all-bonds>>>constraint-algorithm = Lincs>>>unconstrained-start = no>>>lincs-order = 4>>>lincs-iter = 1>>>lincs-warnangle = 30>>Am I missing something?>>>Thanks>>Nisha Patel>-->>>gmx-users mailing list gmx-users@gromacs.org>>>http://lists.gromacs.org/mailman/listinfo/gmx-users>>>Please s
Re: [gmx-users] T-coupling groups
Dear Srinivs,thank you for response. You are right I have already found the source of problem. I have used PEO to name the chain group and forgot that the same group holded for residues. GreetingsZuzanaDňa 03/19/10, jampani srinivas napísal:Dear Zuzana, Recently i have done similar selection, I have got this error only when i miss some atoms or when i have some atoms in both groups. I would suggest you to check your groups carefully or you can make indexes for these selections in VMD and check whether you are missing some atoms from both groups. Srinivs. On Thu, Mar 18, 2010 at 4:55 PM, Zuzana Benkova <zuzana.benk...@savba.sk> wrote: Dear GROMACS users,I have checked the mails in archive which deal with the problem I am facing but did not find the answer what I do wrong. I want to compile a PEO chain centered in box of 2900 water molecules. In my md.mdp the relevant section is as followsTcoupl = nose-hoovertc-grps = PEO SOLtau_t = 0.1 0.1 ref_t = 50 50gen_vel = yesgen_temp = 50 50I have generated an index file where I have defined the PEO group. The [ SOL ] group contains 129-8828 atoms and the [ PEO ] contains 1-128atoms. This matches with the gro file. I tried to prepare a tpr file using grompp -f md.mdp -c PEO18_2900TIP3P_opt.gro -n PEO18_2900TIP3P.ndx -p topol.top -o PEO18_2900TIP3P_50Kand got messageProgram grompp, VERSION 4.0.3Source code file: readir.c, line: 1050Fatal error: 16 atoms are not part of any of the T-Coupling groupsI tried the compilations with 4.0.3 and 4.0.5 versions but the message was the same. I would be really thankful for an advice which can move me further. Thank you in advance. Zuzana--gmx-users mailing list gmx-users@gromacs.orghttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting!Please don't post (un)subscribe requests to the list. Use thewww interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php-- * J. Srinivasa Rao Ph.D.Post-doctoral Research AssociateC/o Prof. Luis R Cruz CruzComputational Biophysics GroupDepartment of PhysicsDrexel University3141 Chestnut StPhiladelphia, PA 19104, USA. Ph: Off: 215-895-1989 Mob: 704-706-4191Web:http://jsrao.web.officelive.com/default.aspx** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] T-coupling groups
Dear GROMACS users, I have checked the mails in archive which deal with the problem I am facing but did not find the answer what I do wrong. I want to compile a PEO chain centered in box of 2900 water molecules. In my md.mdp the relevant section is as follows Tcoupl = nose-hoover tc-grps = PEO SOL tau_t = 0.1 0.1 ref_t = 50 50 gen_vel = yes gen_temp = 50 50 I have generated an index file where I have defined the PEO group. The [ SOL ] group contains 129-8828 atoms and the [ PEO ] contains 1-128atoms. This matches with the gro file. I tried to prepare a tpr file using grompp -f md.mdp -c PEO18_2900TIP3P_opt.gro -n PEO18_2900TIP3P.ndx -p topol.top -o PEO18_2900TIP3P_50K and got message Program grompp, VERSION 4.0.3 Source code file: readir.c, line: 1050 Fatal error: 16 atoms are not part of any of the T-Coupling groups I tried the compilations with 4.0.3 and 4.0.5 versions but the message was the same. I would be really thankful for an advice which can move me further. Thank you in advance. Zuzana -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] topol.top
Dear Mark,I have tried the same processing with version 4.0.5. After that I got the following error messageProgram grompp_s, VERSION 4.0.5Source code file: confio.c, line: 748Fatal error:The spacing of the decimal points in file conf.gro is not consistent for x, y and zMy conf.gro file was constructing according to the required format. I aslo compared it with other gro files, that worked. After replacing replacing of zero .0 by 0.0 the procesing was successful. Thank you for hint.ZuzanaDňa 03/04/10, Mark Abraham napísal:On 5/03/2010 4:08 AM, Zuzana Benkova wrote:>Dear GROMACS users,>I wanted to do a test calculation on a linear unrealistic molecule PPPBC>without any contributions to energy exept of LJ nonbenoded interactions.>I have prepared a topol.top file which I am attaching. After processing>this file with grompp I obtained a message>>WARNING 1 [file topol.top, line 63]:> Too few parameters on line (source file confio.c, line 776)>>Line 63 is the last line of topol.top. I followed the manual and I am>not able to fix the problem. Please could you have a look at this file>and possibly to find out what is missing. Thank you in advanceWhat is your GROMACS version?Mark-- gmx-users mailing list gmx-users@gromacs.orghttp://lists.gromacs.org/mailman/listinfo/gmx-usersPlease search the archive at http://www.gromacs.org/search before posting!Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org.Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] topol.top
Dear Mark,I have used version 4.0.3.ZuzanaDňa 03/04/10, Mark Abraham napísal:On 5/03/2010 4:08 AM, Zuzana Benkova wrote:>Dear GROMACS users,>I wanted to do a test calculation on a linear unrealistic molecule PPPBC>without any contributions to energy exept of LJ nonbenoded interactions.>I have prepared a topol.top file which I am attaching. After processing>this file with grompp I obtained a message>>WARNING 1 [file topol.top, line 63]:> Too few parameters on line (source file confio.c, line 776)>>Line 63 is the last line of topol.top. I followed the manual and I am>not able to fix the problem. Please could you have a look at this file>and possibly to find out what is missing. Thank you in advanceWhat is your GROMACS version?Mark-- gmx-users mailing list gmx-users@gromacs.orghttp://lists.gromacs.org/mailman/listinfo/gmx-usersPlease search the archive at http://www.gromacs.org/search before posting!Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org.Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] topol.top
Dear GROMACS users, I wanted to do a test calculation on a linear unrealistic molecule PPPBC without any contributions to energy exept of LJ nonbenoded interactions. I have prepared a topol.top file which I am attaching. After processing this file with grompp I obtained a message WARNING 1 [file topol.top, line 63]: Too few parameters on line (source file confio.c, line 776) Line 63 is the last line of topol.top. I followed the manual and I am not able to fix the problem. Please could you have a look at this file and possibly to find out what is missing. Thank you in advance Zuzana topol.top Description: Binary 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/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] topol.top
Dear GROMACS users,I wanted to do a test calculation on a linear unrealistic molecule PPPBC without any contributions to energy exept of LJ nonbenoded interactions. I have prepared a topol.top file which I am sending. After processing this file with grompp I obtained a messageWARNING 1 [file topol.top, line 63]: Too few parameters on line (source file confio.c, line 776)Line 63 is the last line of topol.top. I followed the manual and I am not able to fix the problem. Please could you have a look at this file and possibly to find out what is missing. Thank you in advanceZuzana[ defaults ]; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ 1 2 yes 1.0 1.0[ atomtypes ];at. type at.num mass charge ptype sigma epsilonP 1 1 0. A 1 1B 1 1 0. A 2 2C 1 1 0. A 3 1.5[ bondtypes ]; i j func b0 kbP P 1 1 0.P B 1 1 0.B C 1 1 0.[ angletypes ]; i j k func th0 cthP P P 1 0 0.P B C 1 0 0.P P B 1 0 0.[ dihedraltypes ]P P P B 1 0 0 1P P B C 1 0 0 1[ moleculetype ]; Name nrexclProtein 3[ atoms ]; nr type resnr residue atom cgnr charge mass1 P 1 R P 1 0 12 P 1 R P 1 0 13 P 1 R P 1 0 14 B 1 R B 1 0 15 C 1 R C 1 0 1[ bonds ]; ai aj funct c0 c1 c2 c31 2 12 3 13 4 14 5 1[ angles ]; ai aj ak funct c0 c1 c2 c31 2 3 12 3 4 13 4 5 1[ dihedrals ]; ai aj ak al funct1 2 3 4 12 3 4 5 1[ system ]; NameProtein[ molecules ]; Compound #molsProtein 1 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] end-to-end distance
Dear Justin,thank you for response and I am sorry not to define my problem properly. I have used the first alternative, which you discribed and thus obtained the weird resluts. Before I used this alternative I did what you mentioned as the second alternative if I understood it correctly. I have specified the first and the last atoms of each chain as separate groups. But this makes 64 pairs of groups for 64 chairs and I need to apply 64 times g_dist, please, could you correct me if I am wrong? If I am right than it is better to write a script. I am appending the example of my group definitions [ PEO1_&_CH3 ]1 87 173 259 345 431 517 603 689 775 861 947 1033 1119 12051291 1377 1463 1549 1635 1721 1807 1893 1979 2065 2151 2237 2323 2409 24952581 2667 2753 2839 2925 3011 3097 3183 3269 3355 3441 3527 3613 3699 37853871 3957 4043 4129 4215 4301 4387 4473 4559 4645 4731 4817 4903 4989 50755161 5247 5333 5419[ PEON_&_CH3 ]83 169 255 341 427 513 599 685 771 857 943 1029 1115 1201 12871373 1459 1545 1631 1717 1803 1889 1975 2061 2147 2233 2319 2405 2491 25772663 2749 2835 2921 3007 3093 3179 3265 3351 3437 3523 3609 3695 3781 38673953 4039 4125 4211 4297 4383 4469 4555 4641 4727 4813 4899 4985 5071 51575243 5329 5415 5501which provided weird results[ R1 ]1[ R11 ]83[ R2 ] 87 [ R22] 169till [ R64 ] [ R6464 ] pairs which step-by step gave realistic results. Thank you in advanceZuzana.Dňa 02/18/10, "Justin A. Lemkul" napísal:Zuzana Benkova wrote:>Dear GROMACS users,>>I have a system of 64 chains and want to calculate averaged values of end-to-end distance of all chains as well as the averaged radius of gyration from 1ns trajectory. In the case of end-to-end distance I have prepared index file containing one group of the first atoms in ascending order and the second one containing the terminal atoms in ascending order. I have used g_dist but it looks like it combined all pairs between both groups. I have looked at the mailing list but did not find the answer.>g_dist should only be measuring the COM distance between the two selected groups, so I don't know what you mean by "combined all pairs" - perhaps you can provide an example (index groups, relevant output, what you were expecting, and why you think it's wrong)? If your groups contain all starting residues in one, then all ending residues in another, then yes, you're going to get weird results. If you have one chain that is residues 1-100, you should have a group for r_1 and a group for r_100; select those for g_dist analysis. If another chain is residue 101-200, r_101 and r_200 are what you want, etc.>Is it possible to do such analysis using directly GROMACS tools or I need to prepare some scripts with loops running over all chains. Thank you for response in advance.>It certainly should be possible to iteratively use g_dist to measure distances between whatever groups you select. Fairly straightforward, actually, so if you're not getting what you expect, provide the information I asked for above and hopefully someone should be able to figure out what's going wrong.-Justin>Zuzana Benkova>-- Justin A. LemkulPh.D. CandidateICTAS Doctoral ScholarMILES-IGERT TraineeDepartment of BiochemistryVirginia TechBlacksburg, VAjalemkul[at]vt.edu | (540) 231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin-- gmx-users mailing list gmx-users@gromacs.orghttp://lists.gromacs.org/mailman/listinfo/gmx-usersPlease search the archive at http://www.gromacs.org/search before posting!Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org.Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] end-to-end distance
Dear GROMACS users, I have a system of 64 chains and want to calculate averaged values of end-to-end distance of all chains as well as the averaged radius of gyration from 1ns trajectory. In the case of end-to-end distance I have prepared index file containing one group of the first atoms in ascending order and the second one containing the terminal atoms in ascending order. I have used g_dist but it looks like it combined all pairs between both groups. I have looked at the mailing list but did not find the answer. Is it possible to do such analysis using directly GROMACS tools or I need to prepare some scripts with loops running over all chains. Thank you for response in advance.Zuzana Benkova -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] user defined potential
Dear GROMACS users,if I want to use table defined potential for nonbonded interactions I have to do so for all pairs between different grops or is there a possibility to specify just one kind lets say BH potential by tables and to use wdvtype=cut-off for LJ interactions. It seems to me that this is not possible. Could you be so kind and confirm my opinion that if I want to mix BH and LJ potential I have to define all interactions by tables. Zuzana Benkova -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] size dependence of fluctuations
Dear GROMACS users, most likely I am asking a trivial question but I need to be sure about it for calculations of heat capacity based on the fluctuations of energy in canonical ensemble. I am doing simulation of water using TIP4P model. I compare two systems consisting of 216 and 8*216 = 1728 molecules. The expected fluctuations for the larger system should be reduced 8^(1/2)=2.83 times with respect to the fluctuations of the smaller system. Actually, this applies only to the fluctuations in intensive properties such as the temperature, pressure and density while the fluctuations in extensive properties such as energies exceed about 2.83 times the corresponding fluctuations for smaller system. Could you explain me the inverse ratio of fluctuations? I have also one question regarding the heat capacity calculation. If I want to apply the formula for canonical ensemble (-^2)/(kbT^2) than the capacity should be size dependent. I am a bit puzzled about it and any explanation would be very helpful for me. Thanks in advance Zuzana. ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] No default LJ-14 types
Dear GROMACS users, I want to use GROMOS force field for the polyethylene simulations to compare the performance of this force field with those generated for alkanes. I have prepared my own files based on the ffG53a5 files. In itp I used [ defaults ] ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ 1 1 no 1.0 1.0 and in rtp [ bondedtypes ] ; bonds angles dihedrals impropers 2 2 1 2 In my topology file I required nrexcl = 3 in moleculetype section. I included [ pairs ] where all 1-4 pairs were given. When I did the same for polyalanine system in which case I have used the ffG53a5 directly from top library, the simulation run and I got the 1-4 contribution to the potential energy in log file. However in the case of polyethylene after preprocessing using grompp I got error 41 messages for each of 41 pairs of the following kind ERROR 35 [file C44.itp, line 134]: No default LJ-14 types From manual I expect that if gen-pairs is no, 1-4 interaction are taken from pairs section and if yes the 1-4 interaction not presented in pairs section are generated with corresponding fractions as defined in fudgeLJ and fudgeQQ. Previously I removed all the pairs section, simulations run but without 1-4 LJ contribution. I have the same problem with OPLS force field, with which despite the Ryckaert-Bellemans dihedral potential the 1-4 interaction should be considered. I would be very thankful for help. Thank you in advance Zuzana ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] UA simulation of PEO melt
Hi Patrick, Thank you very much for your response. I have just downloaded the paper of which you sent the reference. I have not found other FF parameters except for the torsional one about the C-C bond. I have also some papers which provide good results on PEO simulations (JCP, 124, 234901 (2006); JCP, 102, 9725 (1995).) but I am limited with the order of Ryckaert-Bellemans potential. Unfortunately I do not have any idea how to perform the code modification to extent the torsional expansion. This was the second part of my first mail. I hope somebody will provide me with details necessary to modify the code appropriately and with all the changes associated with that. Greetings Zuzana -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of patrick fuchs Sent: Tuesday, May 12, 2009 3:54 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] UA simulation of PEO melt Hi Zuzana, I'm actually working on the paramaterization of polyethers with the GROMOS developers. Currently in G53a?, there's no such torsion O-C-C-O in GROMOS and I don't advice to use any combination of existing monoethers. I could figure out that they give the wrong free energy of hydration. I hope to have the parameters ready before the end of the year. Meanwhile, you can use the recently optimized parameters for CHARMM (http://dx.doi.org/10.1529/biophysj.108.133025) though they are all-atom. Cheers, Patrick Zuzana Benkova a écrit : > Dear GROMACS users > I want to run simulations of polyethyleneoxide melt. In literature I > have found united atoms force fields that performed well for this kind > of simulation. For dihedral potential I need to extend the > Ryckaert-Bellemans potential up to the order of six. I have looked at > the mailing list and found some information which give advice to change > the code for this kind of potential. But I could not figure out where to > do this changes and how to do them. I would need some detail to do it. I > do not have experience with something like this. > > My second question also concerns PEO. I tried to use GROMOS force field > as well for simulations. I used the parameters from ffG53a5 files. In > ffG53a5bon.itp I am not sure which code of dihedrals sould be used for > C-C-O-C and O-C-C-O and which one for the bond angles. In the case of > bond angle I found type ga_8 as suitable, but it seems me from the > description that it sould be the same for all three bonds in PEO. This > seems to be not OK, since the bending of C-O-C angle is characterized by > larger bending constant. > > I would appreciate any help. Thank you in advance > > Zuzana. > > > > > > > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- ___ new E-mail address: patrick.fu...@univ-paris-diderot.fr Patrick FUCHS Dynamique des Structures et Interactions des Macromolécules Biologiques INTS, INSERM UMR-S665, Université Paris Diderot, 6 rue Alexandre Cabanel, 75015 Paris Tel : +33 (0)1-44-49-30-57 - Fax : +33 (0)1-47-34-74-31 Web Site: http://www.dsimb.inserm.fr/~fuchs ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] UA simulation of PEO melt
Dear GROMACS users I want to run simulations of polyethyleneoxide melt. In literature I have found united atoms force fields that performed well for this kind of simulation. For dihedral potential I need to extend the Ryckaert-Bellemans potential up to the order of six. I have looked at the mailing list and found some information which give advice to change the code for this kind of potential. But I could not figure out where to do this changes and how to do them. I would need some detail to do it. I do not have experience with something like this. My second question also concerns PEO. I tried to use GROMOS force field as well for simulations. I used the parameters from ffG53a5 files. In ffG53a5bon.itp I am not sure which code of dihedrals sould be used for C-C-O-C and O-C-C-O and which one for the bond angles. In the case of bond angle I found type ga_8 as suitable, but it seems me from the description that it sould be the same for all three bonds in PEO. This seems to be not OK, since the bending of C-O-C angle is characterized by larger bending constant. I would appreciate any help. Thank you in advance Zuzana. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] Polyethylene (PE) simulations in Gromacs - please!
Dear Chansoo Kim, It has passed relatively long time since I attempted to use pdb2gmx to build my topology for polyethylene. I prepared the relevant files according to those used for amino acids. I used + and - sign to discern the direction of connectivity. I have encountered dome problems mentioned in the mail but they have not been answered satisfactorily. Later on I wanted to run just united atom simulations and I had next problem with pdb2gmx that always include hydrogen atoms to my topology though I used option which should have disabled this. I decided to build my topology file without pdb2gmx and I applied force field that is not present in GMX directories. _ From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Chansoo Kim Sent: Tuesday, March 03, 2009 2:50 PM To: jalem...@vt.edu; Discussion list for GROMACS users Subject: Re: [gmx-users] Polyethylene (PE) simulations in Gromacs - please! Dear Justin: Thank you for your reply. I was too urgent, so I did not clarify my questions. Sorry about that. I totally understand how topology files (tdb, hdb, and etc..) work, but I do not clearly understand chemical reaction, which I have to define in those files... [Situation] I want to do simulate polyethylene (PE) using Gromacs and OPLS-AA force field... [Topology files and etc] (1) rtp file [ Eth ] [ atoms ] C1opls_136-0.1201 H11 opls_140 0.0601 H12 opls_140 0.0601 C2opls_136-0.1202 H21 opls_140 0.0602 H22 opls_140 0.0602 [ bonds ] C1H11 C1H12 C1C2 C2H21 C2H22 C2+C1 (2) hdb file Eth 2 2 6 H1 C1 C2 +C1 2 6 H2 C2 C1 -C2 (3) -c.tdb file [ Eth ] [ replace ] C1 opls_13512.011 -0.18 [ add ] 34 H1 C1 C2 opls_140 1.008 0.06 [ delete ] H21 H22 (4) -n.tdb file [ Eth ] [ replace ] C2 opls_13512.011 -0.18 [ add ] 34 H2 C2 C1 opls_140 1.008 0.06 [ delete ] H21 H22 (5) input pdb file ATOM 1 C1 Eth 1 1.000 1.540 0.000 ATOM 2 C2 Eth 1 2.456 2.041 0.000 ATOM 3 C1 Eth 2 2.456 3.581 0.000 ATOM 4 C2 Eth 2 3.912 4.083 0.000 ATOM 5 C1 Eth 3 3.912 5.623 0.000 ATOM 6 C2 Eth 3 5.368 6.124 0.000 END [Error] When I did run the pdb2gmx, I got the following error. "Atom -C not found in residue PEth1 while adding hydrogens" [Question #1 and #2] Therefore, what I should define more...? What does the "+" and "-" mean here? [If...] If I change the hdb file as follows, Eth 2 2 6 H1 C1 C2 C1 2 6 H2 C2 C1 C2 After doing pdb2gmx, I got only 12 H-atoms (which means my terminal did NOT work...). And those positions are all (0, 0, 0). Following is the results, LE Giving Russians Opium May Alter Current Situation MODEL1 ATOM 1 C1 PEt 1 1.000 0.000 0.000 1.00 0.00 ATOM 2 H11 PEt 1 0.000 0.000 0.000 1.00 0.00 ATOM 3 H12 PEt 1 0.000 0.000 0.000 1.00 0.00 ATOM 4 C2 PEt 1 2.450 6.000 1.000 1.00 0.00 ATOM 5 H21 PEt 1 0.000 0.000 0.000 1.00 0.00 ATOM 6 H22 PEt 1 0.000 0.000 0.000 1.00 0.00 ATOM 7 C1 PEt 2 2.450 6.000 1.000 1.00 0.00 ATOM 8 H11 PEt 2 0.000 0.000 0.000 1.00 0.00 ATOM 9 H12 PEt 2 0.000 0.000 0.000 1.00 0.00 ATOM 10 C2 PEt 2 3.910 2.000 3.000 1.00 0.00 ATOM 11 H21 PEt 2 0.000 0.000 0.000 1.00 0.00 ATOM 12 H22 PEt 2 0.000 0.000 0.000 1.00 0.00 ATOM 13 C1 PEt 3 3.910 2.000 3.000 1.00 0.00 ATOM 14 H11 PEt 3 0.000 0.000 0.000 1.00 0.00 ATOM 15 H12 PEt 3 0.000 0.000 0.000 1.00 0.00 ATOM 16 C2 PEt 3 5.360 8.000 4.000 1.00 0.00 ATOM 17 H21 PEt 3 0.000 0.000 0.000 1.00 0.00 ATOM 18 H22 PEt 3 0.000 0.000 0.000 1.00 0.00 TER ENDMDL [Question #3 from If... section ] I guess that I have to change hdb and tdb files. Would you please give some guide on that...? Thank you for your care! Sincerely yours, C Kim On Tue, Mar 3, 2009 at 8:35 AM, Justin A. Lemkul wrote: Chansoo Kim wrote: Dear Dr. Benkova and others: I am C. Kim and trying to simulation polymer system. Since I guessed that polyethylene (PE) is a simple system, it could be not that hard to simulate it in Gromacs. Trying to do, I have read Dr. Benkova's articles in gmx-users mailing list to tackle my problems. Sorry to say, I
RE: [gmx-users] running a simulation without production
-Original Message-
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED]
On Behalf Of Zuzana Benkova
Sent: Tuesday, November 04, 2008 3:11 PM
To: 'Discussion list for GROMACS users'
Subject: RE: [gmx-users] running a simulation without production
Dear Mark,
Thank you very much for valuable advice.
Previously, I run some simulations and I obtained what I had expected. For
instance, instead of the plate I have just used one single chain which was
treated as frozen and the simulations were running. I obtained all output
files containing appropriate information.
I have GMX version 3.3.3. I have just tried gmxtest.pl test first in sthe
ingle precision. The output I got was
All 16 simple tests PASSED
FAILED. Check files in dec+water
FAILED. Check files in fe_test
2 out of 14 complex tests FAILED
All 63 kernel tests PASSED
All 45 pdb2gmx tests PASSED
I am not very familiar with programming language C++. As I wanted to test
also the double precision I did some changes in the gmxtest.pl file. I am
not sure if I did it correctly. I have installed GMX with _mpi suffix, so I
have changed the sub setup_vars section
sub setup_vars {
my $mdprefix = "";
if ( $parallel > 0 ) {
$mdprefix = "mpirun -c $parallel ";
}
if ( $double > 0 ) {
$grompp = "grompp_mpi";
$mdrun = $mdprefix . "mdrun_mpi";
$ref= "reference_d";
}
and after applying command gmxtest.pl -double all I have obtained
sh: line 1: 30240 Segmentation fault mdrun_mpi >mdrun.out 2>&1
FAILED. Check files in rb1
1 out of 16 simple tests FAILED
All 14 complex tests PASSED
All 63 kernel tests PASSED
All 45 pdb2gmx tests PASSED
In the case of the single precision test I can not figure out the error
since I do not have any new files produced after the test in corresponding
directories. In the case of double precision test I have also log file in
rb1 directory which has been terminated exactly in the same way as my
attempts to run simulation of plate-chain system.
Please, could you give me some explanation and hints how to proceed further?
It would be very helpful for me. I have checked the mailing list but did not
find something that could help me. Thank you in advance.
Zuzana
-Original Message-
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED]
On Behalf Of Mark Abraham
Sent: Monday, November 03, 2008 9:55 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] running a simulation without production
Zuzana Benkova wrote:
> I have tried also running this job without user specified potential,
> with relaxed plate, with pbc=no and some other attempts, but I always
> failed in the same way. I would be very thankful for suggestions how to
> cope with this problem.
Do other simulations run? Try one of the tutorials or gmxtest.pl.
Mark
___
gmx-users mailing listgmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
___
gmx-users mailing listgmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
___
gmx-users mailing listgmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] running a simulation without production
_ From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Zuzana Benkova Sent: Monday, November 03, 2008 5:49 PM To: gmx-users@gromacs.org Subject: [gmx-users] running a simulation without production Dear GROMACS users, I want to simulate a system consisting of a plate modeled by atoms (5000 atoms) and a polyethylene chain (80 carbons). The plate is frozen and I am using tabulated potentials. In this system, the considered interactions are chain-chain and chain-plate. There are no electrostatic interactions. The system is placed in a box, with dimensions corresponding to the dimensions of plate and substantially larger height. My md.mdp file is as follows cpp = cpp define = integrator = md dt = 0.002 nsteps = 7500 nstcomm = 1 comm_mode = None nstxout = 10 nstvout = 10 nstfout = 10 nstxtcout = 10 nstlog = 10 nstenergy = 10 energygrps = Chain Plate freezegrps = Plate freezedim = Y Y Y energygrp_excl = Plate Plate energygrp_table = Chain Chain Chain Plate nstlist = 1 ns_type = simple rlist = 0.4 pbc = xyz vdw-type= User rvdw= 0.4 coulombtype = cut-off rcoulomb= 0.1 Tcoupl = nose-hoover tc-grps = System tau_t = 0.1 ref_t = 450 gen_vel = yes gen_temp= 450 constraints = none pcoupl = no After launching this job the process is running but there is no trajectory to be produced. The log file finishes in the section containing following information energygrp_flags[ 0]: 2 2 energygrp_flags[ 1]: 2 1 I have tried also running this job without user specified potential, with relaxed plate, with pbc=no and some other attempts, but I always failed in the same way. I would be very thankful for suggestions how to cope with this problem. Greetings Zuzana ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] running a simulation without production
Dear Mark,
Thank you very much for valuable advice.
Previously, I run some simulations and I obtained what I had expected. For
instance, instead of the plate I have just used one single chain which was
treated as frozen and the simulations were running. I obtained all output
files containing appropriate information.
I have GMX version 3.3.3. I have just tried gmxtest.pl test first in sthe
ingle precision. The output I got was
All 16 simple tests PASSED
FAILED. Check files in dec+water
FAILED. Check files in fe_test
2 out of 14 complex tests FAILED
All 63 kernel tests PASSED
All 45 pdb2gmx tests PASSED
I am not very familiar with programming language C++. As I wanted to test
also the double precision I did some changes in the gmxtest.pl file. I am
not sure if I did it correctly. I have installed GMX with _mpi suffix, so I
have changed the sub setup_vars section
sub setup_vars {
my $mdprefix = "";
if ( $parallel > 0 ) {
$mdprefix = "mpirun -c $parallel ";
}
if ( $double > 0 ) {
$grompp = "grompp_mpi";
$mdrun = $mdprefix . "mdrun_mpi";
$ref= "reference_d";
}
and after applying command gmxtest.pl -double all I have obtained
sh: line 1: 30240 Segmentation fault mdrun_mpi >mdrun.out 2>&1
FAILED. Check files in rb1
1 out of 16 simple tests FAILED
All 14 complex tests PASSED
All 63 kernel tests PASSED
All 45 pdb2gmx tests PASSED
In the case of the single precision test I can not figure out the error
since I do not have any new files produced after the test in corresponding
directories. In the case of double precision test I have also log file in
rb1 directory which has been terminated exactly in the same way as my
attempts to run simulation of plate-chain system.
Please, could you give me some explanation and hints how to proceed further?
It would be very helpful for me. I have checked the mailing list but did not
find something that could help me. Thank you in advance.
Zuzana
-Original Message-
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED]
On Behalf Of Mark Abraham
Sent: Monday, November 03, 2008 9:55 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] running a simulation without production
Zuzana Benkova wrote:
> I have tried also running this job without user specified potential,
> with relaxed plate, with pbc=no and some other attempts, but I always
> failed in the same way. I would be very thankful for suggestions how to
> cope with this problem.
Do other simulations run? Try one of the tutorials or gmxtest.pl.
Mark
___
gmx-users mailing listgmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
___
gmx-users mailing listgmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] running a simulation without production
Dear GROMACS users, I want to simulate a system consisting of a plate modeled by atoms (5000 atoms) and a polyethylene chain (80 carbons). The plate is frozen and I am using tabulated potentials. In this system, the considered interactions are chain-chain and chain-plate. There are no electrostatic interactions. The system is placed in a box, with dimensions corresponding to the dimensions of plate and substantially larger height. My md.mdp file is as follows cpp = cpp define = integrator = md dt = 0.002 nsteps = 7500 nstcomm = 1 comm_mode = None nstxout = 10 nstvout = 10 nstfout = 10 nstxtcout = 10 nstlog = 10 nstenergy = 10 energygrps = Chain Plate freezegrps = Plate freezedim = Y Y Y energygrp_excl = Plate Plate energygrp_table = Chain Chain Chain Plate nstlist = 1 ns_type = simple rlist = 0.4 pbc = xyz vdw-type= User rvdw= 0.4 coulombtype = cut-off rcoulomb= 0.1 Tcoupl = nose-hoover tc-grps = System tau_t = 0.1 ref_t = 450 gen_vel = yes gen_temp= 450 constraints = none pcoupl = no After launching this job the process is running but there is no trajectory to be produced. The log file finishes in the section containing following information energygrp_flags[ 0]: 2 2 energygrp_flags[ 1]: 2 1 I have tried also running this job without user specified potential, with relaxed plate, with pbc=no and some other attempts, but I always failed in the same way. I would be very thankful for suggestions how to cope with this problem. Greetings Zuzana ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] g_angle
Dear GMX users, I want to analyse th ebond angle. I have used mk_angndx -s md1.tpr -n angle.ndx to prepare an index for g_angle. After g_angle -f md1.xtc -s md1.tpr -n angle.ndx I have obtained Software inconsistency error: Not supported in get_stx_coordnum Most likely this is a trivial question and I did some stupid mistake but I would be thankful for help. Thank you in advance Zuzana ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] angle analysis
Dear GMX users, I want to analyse th ebond angle. I have used mk_angndx -s md1.tpr -n angle.ndx to prepare an index for g_angle. After g_angle -f md1.xtc -s md1.tpr -n angle.ndx I have obtained Software inconsistency error: Not supported in get_stx_coordnum Most likely this is a trivial question and I did some stupid mistake but I would be thankful for help. Thank you in advance Zuzana ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] problem in hdb file
Dear GMX users, I want to prepare .gro and topology file starting from the .pdb file for a polyethylene chain , whose residue is not defined in .rtp, .hdb. and .tdb files. I have defined a new residue in ffoplsaa.rtp file as follows [ Eth ] [ atoms ] C1opls_136-0.1201 H11 opls_140 0.0601 H12 opls_140 0.0601 C2opls_136-0.1202 H21 opls_140 0.0602 H22 opls_140 0.0602 [ bonds ] C1H11 C1H12 C1C2 C2H21 C2H22 C2+C1 In ffoplsaa.hdb I defined it as Eth 2 2 6 H1 C1 C2 +C1 2 6 H2 C2 C1 -C2 At this point I have to note that the presence of the last control atoms in this file has not influenced the process. In ffoplsaa-n.tdb file I have added [ Eth ] [ replace ] C2 opls_13512.011 -0.18 [ add ] 34 H2 C2 C1 opls_140 1.008 0.06 [ delete ] H21 H22 and in ffoplsaa-c.tdb file I have added [ Eth ] [ replace ] C1 opls_13512.011 -0.18 [ add ] 34 H1 C1 C2 opls_140 1.008 0.06 [ delete ] H21 H22 After using pdb2gmx -f input.pdb I have obtained following message Opening library file ffoplsaa.rtp Opening library file /usr/local/share/gromacs/gromacs-3.3/share/top/aminoacids.dat Reading hexane.pdb... Read 6 atoms Opening library file /usr/local/share/gromacs/gromacs-3.3/share/top/xlateat.dat 26 out of 26 lines of xlateat.dat converted succesfully Analyzing pdb file There are 1 chains and 0 blocks of water and 3 residues with 6 atoms chain #res #atoms 1 ' ' 3 6 All occupancies are one Opening library file /usr/local/share/gromacs/gromacs-3.3/share/top/ffoplsaa.atp Atomtype 817 Reading residue database... (ffoplsaa) Opening library file ffoplsaa.rtp Residue 59 Sorting it all out... Opening library file ffoplsaa.hdb Error in hdb file: nah = 41 line = '' Opening library file ffoplsaa-n.tdb Opening library file ffoplsaa-c.tdb Back Off! I just backed up topol.top to ./#topol.top.8# Processing chain 1 (6 atoms, 3 residues) There are 0 donors and 0 acceptors There are 0 hydrogen bonds Checking for duplicate atoms Opening library file /usr/local/share/gromacs/gromacs-3.3/share/top/specbond.dat 5 out of 5 lines of specbond.dat converted succesfully N-terminus: Eth C-terminus: Eth Segmentation fault Could you specify what means Error in hdb file: nah = 41 line = '' and what is the problem with segmentation. My input structure in .pdb file is as follows ATOM 1 C1 Eth 1 1.000 1.540 0.000 ATOM 2 C2 Eth 1 2.456 2.041 0.000 ATOM 3 C1 Eth 2 2.456 3.581 0.000 ATOM 4 C2 Eth 2 3.912 4.083 0.000 ATOM 5 C1 Eth 3 3.912 5.623 0.000 ATOM 6 C2 Eth 3 5.368 6.124 0.000 END Thank you for help in advance Best regards Zuzana ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Polyethylene
Dear GMX users, I want to prepare .gro and topology file starting from the .pdb file for a polyethylene chain , whose residue is not defined in .rtp, .hdb. and .tdb files. I have defined a new residue in ffoplsaa.rtp file as follows [ Eth ] [ atoms ] C1opls_136-0.1201 H11 opls_140 0.0601 H12 opls_140 0.0601 C2opls_136-0.1202 H21 opls_140 0.0602 H22 opls_140 0.0602 [ bonds ] C1H11 C1H12 C1C2 C2H21 C2H22 C2+C1 In ffoplsaa.hdb I defined it as Eth 2 2 6 H1 C1 C2 +C1 2 6 H2 C2 C1 -C2 At this point I have to note that the presence of the last control atoms in this file has not influenced the process. In ffoplsaa-n.tdb file I have added [ Eth ] [ replace ] C2 opls_13512.011 -0.18 [ add ] 34 H2 C2 C1 opls_140 1.008 0.06 [ delete ] H21 H22 and in ffoplsaa-c.tdb file I have added [ Eth ] [ replace ] C1 opls_13512.011 -0.18 [ add ] 34 H1 C1 C2 opls_140 1.008 0.06 [ delete ] H21 H22 After using pdb2gmx -f input.pdb I have obtained following message Opening library file ffoplsaa.rtp Opening library file /usr/local/share/gromacs/gromacs-3.3/share/top/aminoacids.dat Reading hexane.pdb... Read 6 atoms Opening library file /usr/local/share/gromacs/gromacs-3.3/share/top/xlateat.dat 26 out of 26 lines of xlateat.dat converted succesfully Analyzing pdb file There are 1 chains and 0 blocks of water and 3 residues with 6 atoms chain #res #atoms 1 ' ' 3 6 All occupancies are one Opening library file /usr/local/share/gromacs/gromacs-3.3/share/top/ffoplsaa.atp Atomtype 817 Reading residue database... (ffoplsaa) Opening library file ffoplsaa.rtp Residue 59 Sorting it all out... Opening library file ffoplsaa.hdb Error in hdb file: nah = 41 line = '' Opening library file ffoplsaa-n.tdb Opening library file ffoplsaa-c.tdb Back Off! I just backed up topol.top to ./#topol.top.8# Processing chain 1 (6 atoms, 3 residues) There are 0 donors and 0 acceptors There are 0 hydrogen bonds Checking for duplicate atoms Opening library file /usr/local/share/gromacs/gromacs-3.3/share/top/specbond.dat 5 out of 5 lines of specbond.dat converted succesfully N-terminus: Eth C-terminus: Eth Segmentation fault Could you specify what means Error in hdb file: nah = 41 line = '' and what is the problem with segmentation. My input structure in .pdb file is as follows ATOM 1 C1 Eth 1 1.000 1.540 0.000 ATOM 2 C2 Eth 1 2.456 2.041 0.000 ATOM 3 C1 Eth 2 2.456 3.581 0.000 ATOM 4 C2 Eth 2 3.912 4.083 0.000 ATOM 5 C1 Eth 3 3.912 5.623 0.000 ATOM 6 C2 Eth 3 5.368 6.124 0.000 END Thank you for help in advance Best regards Zuzana ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Polyethylene
Dear GMX users, I want to prepare .gro and topology files starting from the .pdb file for a polyethylene chain , whose residue is not defined in .rtp, .hdb. and .tdb files. I have defined a new residue in ffoplsaa.rtp file as follows [ Eth ] [ atoms ] C1opls_136-0.1201 H11 opls_140 0.0601 H12 opls_140 0.0601 C2opls_136-0.1202 H21 opls_140 0.0602 H22 opls_140 0.0602 [ bonds ] C1H11 C1H12 C1C2 C2H21 C2H22 C2+C1 In ffoplsaa.hdb I defined it as Eth 2 2 6 H1 C1 C2 +C1 2 6 H2 C2 C1 -C2 At this point I have to note that the presence of the last control atoms in this file has not influenced the process. In ffoplsaa-n.tdb file I have added [ Eth ] [ replace ] C2 opls_13512.011 -0.18 [ add ] 34 H2 C2 C1 opls_140 1.008 0.06 [ delete ] H21 H22 and in ffoplsaa-c.tdb file I have added [ Eth ] [ replace ] C1 opls_13512.011 -0.18 [ add ] 34 H1 C1 C2 opls_140 1.008 0.06 [ delete ] H11 H12 After using pdb2gmx -f input.pdb I have obtained following message Opening library file ffoplsaa.rtp Opening library file /usr/local/share/gromacs/gromacs-3.3/share/top/aminoacids.dat Reading hexane.pdb... Read 6 atoms Opening library file /usr/local/share/gromacs/gromacs-3.3/share/top/xlateat.dat 26 out of 26 lines of xlateat.dat converted succesfully Analyzing pdb file There are 1 chains and 0 blocks of water and 3 residues with 6 atoms chain #res #atoms 1 ' ' 3 6 All occupancies are one Opening library file /usr/local/share/gromacs/gromacs-3.3/share/top/ffoplsaa.atp Atomtype 817 Reading residue database... (ffoplsaa) Opening library file ffoplsaa.rtp Residue 59 Sorting it all out... Opening library file ffoplsaa.hdb Error in hdb file: nah = 41 line = '' Opening library file ffoplsaa-n.tdb Opening library file ffoplsaa-c.tdb Back Off! I just backed up topol.top to ./#topol.top.8# Processing chain 1 (6 atoms, 3 residues) There are 0 donors and 0 acceptors There are 0 hydrogen bonds Checking for duplicate atoms Opening library file /usr/local/share/gromacs/gromacs-3.3/share/top/specbond.dat 5 out of 5 lines of specbond.dat converted succesfully N-terminus: Eth C-terminus: Eth Segmentation fault Could you specify what means Error in hdb file: nah = 41 line = '' and what is the problem with segmentation. My input structure in .pdb file is as follows ATOM 1 C1 Eth 1 1.000 1.540 0.000 ATOM 2 C2 Eth 1 2.456 2.041 0.000 ATOM 3 C1 Eth 2 2.456 3.581 0.000 ATOM 4 C2 Eth 2 3.912 4.083 0.000 ATOM 5 C1 Eth 3 3.912 5.623 0.000 ATOM 6 C2 Eth 3 5.368 6.124 0.000 END Thank you for help in advance Best regards Zuzana ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] Temperature increase
Dear Mark, thank you very much for prompt reply, I am sorry but I did mistake in my first e-mail I have run an NVE simulation of decamer of glycin first with PBC (coulombtype=PME)and later without PBC (coulombtype=Cut-off). Zuzana -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Mark Abraham Sent: Thursday, May 03, 2007 3:46 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Temperature increase Zuzana Benkova wrote: > I have run an NVE simulation of decamer of glycin first with PBC > (coulombtype=Cut-off) and later without PBC (coulombtype=PME). You can't have a non-periodic system with PME. > The > gen-temp was set to 300K with option gen-vel=yes. The temperature start > to raise during simulation and finaly the following messages appeared in > log file > > Shake did not converge in 1000 steps > > i mi j mj before after should be > >66 14.01 67 1.01 0.10100 0.10318 0.10100 > > Constraint error in algorithm Shake at step 980454 > > Wrote pdb files with previous and current coordinates > > How can I cope with this? We can't tell, because the above description is not self-consistent. In any case you haven't defined your topology, or minimized your structure or equilibrated properly. Then some bad structural element is causing a region to have too much energy which is breaking structures. Search the mailing list archives for suggested equilibration regimes, or read relevant literature examples, or do tutorial material. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Temperature increase
I have run an NVE simulation of decamer of glycin first with PBC (coulombtype=Cut-off) and later without PBC (coulombtype=PME). The gen-temp was set to 300K with option gen-vel=yes. The temperature start to raise during simulation and finaly the following messages appeared in log file Shake did not converge in 1000 steps i mi j mj before after should be 66 14.01 67 1.01 0.10100 0.10318 0.10100 Constraint error in algorithm Shake at step 980454 Wrote pdb files with previous and current coordinates How can I cope with this? Tahnk you in advance Zuzana ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] (no subject)
test ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] polyethelenes
Hello gmx-users, I have only little experiences with Gromacs and I am trying to run MD simulations on polyethelenes. I tried to modify the ffoplsaa.rtp and ffoplsaa.hdb where I have added my own residui. The addition in ffoplsaa.rtp is as follows ; Ethyle - CH3-CH2 the first unit in polyethylenes [ TTH ] [ atoms ] C1 opls_135 -0.180 1 HA1 opls_140 0.060 1 HA2 opls_140 0.060 1 HA3 opls_140 0.060 1 C2 opls_136 -0.120 2 HB1 opls_140 0.060 2 HB2 opls_140 0.060 2 [ bonds ] C1 HA1 C1 HA2 C1 HA3 C1 C2 C2 HB1 C2 HB2 ; Ethylene - CH2-CH2 central parts of polyetylens (CnHm) [ ETH ] [ atoms ] C1 opls_135 -0.180 1 HA1 opls_140 0.060 1 HA2 opls_140 0.060 1 C2 opls_136 -0.120 2 HB1 opls_140 0.060 2 HB2 opls_140 0.060 2 [ bonds ] C1 HA1 C1 HA2 C1 C2 C2 HB1 C2 HB2 ; Ethyle - CH2-CH3 the last unit in polyethylenes [ THT ] [ atoms ] C1 opls_135 -0.180 1 HA1 opls_140 0.060 1 HA2 opls_140 0.060 1 C2 opls_136 -0.120 2 HB1 opls_140 0.060 2 HB2 opls_140 0.060 2 HB3 opls_140 0.060 2 [ bonds ] C1 HA1 C1 HA2 C1 C2 C2 HB1 C2 HB2 C2 HB3 and the addition in ffoplsaa.hdb file is as follows TTH 2 3 4 HA C1 C2 HB +C2 2 6 HB C2 C1 +C1 ETH 2 2 6 HA C1 -C2 C2 2 6 HB C2 C1 +C1 THT 2 2 6 HA C1 -C2 C2 3 4 HB C2 C1 -C2 HA I have also added these three residui (TTH, ETH, and THT) into aminoacids.dat file. My attempt to convert the pdb file into the gro and top files using pdb2gmx I got following error messages Error in hdb file: nah = 38 line = '' and Fatal error: Atom HB not found in residue TTH1 while adding hydrogens The pdb file is attached in this mail. I would be thankful for any help. Thank you in advance. Greetings Zuzana Polyethylene.pdb Description: Binary data ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
