[gmx-users] gmxcheck : Magic Number Error in XTC file (read 0, should be 1995)
Dear Gromacs Users, I have a trajectory of 2microsecond. I am trying to use gmxcheck to analyse trajectory but I am getting following error; Program gmxcheck, VERSION 4.6.5 Source code file: /home/suman/sources/gromacs-4.6.5/src/gmxlib/xtcio.c, line: 92 Fatal error: Magic Number Error in XTC file (read 0, should be 1995) I have seen similar questions in the mailing list describing the trajectory may be corrupted. If its true in all the cases of this error, Is there any way to recover the trajectory? Please provide suggestion to solve the error. Regards, Amit = Amit R. Kumawat Junior Research Fellow, Physical Materials Chemistry Division CSIR-National Chemical Laboratory Pune, INDIA = -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] gmxcheck : Magic Number Error in XTC file (read 0, should be 1995)
On 2014-12-24 15:33, Amit Kumawat wrote: Dear Gromacs Users, I have a trajectory of 2microsecond. I am trying to use gmxcheck to analyse trajectory but I am getting following error; Program gmxcheck, VERSION 4.6.5 Source code file: /home/suman/sources/gromacs-4.6.5/src/gmxlib/xtcio.c, line: 92 Fatal error: Magic Number Error in XTC file (read 0, should be 1995) I have seen similar questions in the mailing list describing the trajectory may be corrupted. If its true in all the cases of this error, Is there any way to recover the trajectory? Please provide suggestion to solve the error. start with trjconv -f old.xtc -o new.xtc to see how much is corrupt. Regards, Amit = Amit R. Kumawat Junior Research Fellow, Physical Materials Chemistry Division CSIR-National Chemical Laboratory Pune, INDIA = -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] initial velocities
Dear all, I want to apply an initial velocity to my system. Is there a possible way rather than gen_vel in which I can chose my own wanted velocities? And if so, how can I introduce the vx,vy and vz for the atoms? thank you -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] initial velocities
Hi Mah Maz, The easiest way is to write a .gro file with the velocities you want and use that as input. Cheers, Tsjerk On Dec 24, 2014 5:14 PM, mah maz mahma...@gmail.com wrote: Dear all, I want to apply an initial velocity to my system. Is there a possible way rather than gen_vel in which I can chose my own wanted velocities? And if so, how can I introduce the vx,vy and vz for the atoms? thank you -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] initial velocities
Thank you very much Tsjerk! As far as I know .gro files are coordinate ones, containing the structure of the system. How is it possible to make difference between x,y and z AND vx,vy and vz? Should I write the file like coordinate format? Regards, Mah On Wed, Dec 24, 2014 at 7:44 PM, mah maz mahma...@gmail.com wrote: Dear all, I want to apply an initial velocity to my system. Is there a possible way rather than gen_vel in which I can chose my own wanted velocities? And if so, how can I introduce the vx,vy and vz for the atoms? thank you -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] initial velocities
Hi Mah, You can add velocities after the coordinates, in the same format, usually %8.3f Cheers, Tsjerk On Dec 24, 2014 7:41 PM, mah maz mahma...@gmail.com wrote: Thank you very much Tsjerk! As far as I know .gro files are coordinate ones, containing the structure of the system. How is it possible to make difference between x,y and z AND vx,vy and vz? Should I write the file like coordinate format? Regards, Mah On Wed, Dec 24, 2014 at 7:44 PM, mah maz mahma...@gmail.com wrote: Dear all, I want to apply an initial velocity to my system. Is there a possible way rather than gen_vel in which I can chose my own wanted velocities? And if so, how can I introduce the vx,vy and vz for the atoms? thank you -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] initial velocities
On 12/24/14 2:17 PM, Tsjerk Wassenaar wrote: Hi Mah, You can add velocities after the coordinates, in the same format, usually %8.3f %8.4f for velocities, coordinates are %8.3f :) http://manual.gromacs.org/online/gro.html -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Error in topology using g_x2top
On 12/24/14 1:39 AM, Rajan Kumar wrote: Hi all, I am trying to study wetting of water on Graphene oxide(GO). My structure has functional group in form of Hydroxyl and epoxide group on only one side of the Graphene sheet. Also I have added water molecules in form of spherical droplet on the same side of the sheet. Since my simulation will be periodic in the plane of the GO sheet, I have not capped edges with hydrogen. I have created atomtypes.atp and atomname2type.n2t based on connectivity of individuals atoms and added them to force field file(oplsaa_GO.ff) in the working directory(Thanks Justin Lemkul for Suggestion). Also, I have copied original opls-aa ffnonded and ffnonbonded topology files to my working directory. Have a look at my files here https://www.dropbox.com/sh/rtxg36y4pv2zwto/AADoQ_Y239XuSXK7-_4PNGJ_a?dl=0 After creating .gro using editconf, I generate topology using g_x2top which gives me following error. g_x2top -f conf.gro -o topol.top -ff oplsaa_GO Opening force field file ./oplsaa_GO.ff/atomname2type.n2t There are 11 name to type translations in file ./oplsaa_GO.ff Generating bonds from distances... atom 420 Can not find forcefield for atom OS-9 with 5 bonds Can not find forcefield for atom OH-10 with 8 bonds Can not find forcefield for atom HO-11 with 8 bonds Can not find forcefield for atom OS-20 with 11 bonds Can not find forcefield for atom OH-21 with 16 bonds Can not find forcefield for atom HO-22 with 10 bonds Can not find forcefield for atom OS-31 with 12 bonds Can not find forcefield for atom OH-32 with 10 bonds Can not find forcefield for atom HO-33 with 13 bonds Can not find forcefield for atom OS-42 with 6 bonds Can not find forcefield for atom OH-43 with 13 bonds Can not find forcefield for atom OS-325 with 4 bonds Can not find forcefield for atom OH-326 with 7 bonds Can not find forcefield for atom HO-327 with 8 bonds - -- Can not find forcefield for atom HW2-414 with 13 bonds Can not find forcefield for atom OW-415 with 4 bonds Can not find forcefield for atom HW1-416 with 3 bonds Can not find forcefield for atom HW2-417 with 2 bonds Can not find forcefield for atom OW-418 with 20 bonds Can not find forcefield for atom HW1-419 with 9 bonds Can not find forcefield for atom HW2-420 with 6 bonds --- Program g_x2top, VERSION 4.5.5 Source code file: g_x2top.c, line: 206 Fatal error: Could only find a forcefield type for 238 out of 420 atoms Please help me out here. Something is very bizarre with the input coordinates or the .n2t file, but a quick look at the files doesn't suggest what it is. If g_x2top is detecting 20 (yikes!) bonds for a water oxygen atom, that suggests something is catastrophically wrong somewhere. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] initial velocities
Many thanks Tsjerk and Justin! You both helped alot. Regards, Mah On Wed, Dec 24, 2014 at 10:10 PM, mah maz mahma...@gmail.com wrote: Thank you very much Tsjerk! As far as I know .gro files are coordinate ones, containing the structure of the system. How is it possible to make difference between x,y and z AND vx,vy and vz? Should I write the file like coordinate format? Regards, Mah On Wed, Dec 24, 2014 at 7:44 PM, mah maz mahma...@gmail.com wrote: Dear all, I want to apply an initial velocity to my system. Is there a possible way rather than gen_vel in which I can chose my own wanted velocities? And if so, how can I introduce the vx,vy and vz for the atoms? thank you -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Pulling code
Dear Justin A. Lemkul, I want to use pulling code for calculate the PMF of a molecule at the across the DMPC, but i can't obtained a large pull across the membrane my pulling code was: ; Pull code pull= umbrella pull_geometry= position pull_dim= N N Y pull_start = yes; define initial COM distance 0 pull_ngroups= 1 pull_group0= DMPC pull_group1= QBH pull_k1= 1000 ; kJ mol^-1 nm^-2 pull_vec1= 0 0 0.5 after perl distances.pl step i obtained a summary.dat file. but in this file pulling was very low, just about 0.3nm. My molecule name is QBH and is out of membrane at bulk of the water and i want to pull it until center of bilayer. what must i do? Regards -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] length of beta sheet
Hi everyone, I would like to calculate length of beta sheet. Is this any automatic tool to serve the purpose? To elaborate, I am aware that dssp can give me whether the residue is in beta sheet (E) or not at each time frame but I want to know exactly how many hydrogen bonds are formed by each residue in E (and not just E if minimum criterion of two hydrogen bonds is satisfied by DSSP). From this I would like to calculate length of beta sheet. Any help is highly appreciated. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Questions about CO2.
Dear all, I went through the mails about the use of virtual sites for representing linear molecules like CO2. I also read that GROMACS cannot handle angle bending potentials at 180 degrees in an appropriate manner. My system consists of EPM2-CO2 dissollved in TIP4- H2O. I made topology files for CO2 with virtual sites and also made another topology without the use of virtual sites providing the equilibrium angle (180) and the bending force constant. Both these are given at the end. I am trying to use the EPM2 model for CO2 reported in* J. Phys. Chem. 1995,99, 12021-12024* by *Jonathan G. Harris and Kwong H. Yung* under the title Carbon Dioxide's Liquid-Vapor Coexistence Curve and Critical Properties As Predicted by a Simple Molecular Model. I have the following questions; (i) I am using gromacs 4.6.5. Is the problem related to treating angle bending potentials for linear molecules solved in later versions of gromacs? (ii) The authors Harris and Yung stress that their model is flexible in terms of bending in the abstract of their article. So if I build this model using virtual sites then I believe I am neglecting the flexibility. Also while using virtual sites the model looks more like a dimer with two point masses, instead of a a three point EPM2 model. So can I call this an EPM2 model any more.? Do you think introducing virtual sites affects the results which are expected from a simple looking EPM2 model, with three charged-Lennard-Jones point masses with a flexible angle. I appreciate (and often surprised by) the fact that a simple model like EPM2 which can be specified by a total of just nine parameters can accurately predict the properties of CO2 at supercritical conditions which otherwise may a be a very intricate condensed system to study. This prompts me to think that any small change in the model can impart an error that can get magnified for a system of thousands of molecules. (iii) I found that I am getting highly positive energy values when using the topology built using virtual sites. To add to this I am forced to use very short time steps (0.2 fs) for simulations, since with 2fs, system was unstable which I believe has to do with the positive energy and high force values. Whereas, using the topology built in the usual way without virtual sites, I get negative energy values and simulations could easily be performed using a 2fs time step (system may be more stable) . I checked the angles in this case at the final state of the system, and found them lying between 175 to 180 degrees, which I am not sure if it is all right. Is this slight deviation from 180 degree caused by the failure of GROMACS to maintain linearity? Or, is it perfectly normal since the model itself is flexible.? Please share your views. Regards, Sujith. *TOPOLOGY USING VIRTUAL SITES:* [atomtypes] ; name mass charge ptypesigma epsilon D 22.0049 0. A 0. 0. CA 0.0.6512 A 0.2757 0.2339 CO 0. -0.3256 A 0.3033 0.6695 [moleculetype] ; name nrexcl CO22 [atoms] ; nr type resnr residue atom cgnr charge mass 1 D 1 CO2 D1 10. 22.0049 2 D 1 CO2 D2 10. 22.0049 3 CA1 CO2CA 10.6512 0. 4 CO1 CO2OC11 -0.3256 0. 5 CO1 CO2OC21 -0.3256 0. [constraints] ; i j funct doc 1 2 1 0.195948 [virtual_sites2] ; i j k funct a 3 1 2 1 0.5 4 1 2 1 1.08638006 5 2 1 1 1.08638006 *TOPOLOGY WITHOUT VIRTUAL SITES:* [ defaults ] ; nbfunc comb-rule gen-pairsfudgeLJ fudgeQQ 1 2 no 1.0 1.0 [atomtypes] ;name mass charge ptype sigma epsilon CA 12.011000.6512 A 0.27570.2339 CO 15.99940 -0.3256 A 0.30330.6695 [ nonbond_params ] ; i j funct sigmaepsilon CA CO10.2892 0.3955 [moleculetype] ; name nrexcl CO22 [atoms] ; nr type resnr residue atom cgnr charge mass 1 CA1 CO2 CA 1 0.6512 12.0110 2 CO1 CO2 OC1 1 -0.3256 15.9994 3 CO1 CO2 OC2 1 -0.3256 15.9994 [angles] ; i j k funct ao ak 3 1 2 1 180 1236 [constraints] ; i j funct doc 1 2 1 0.1149 1 3 1 0.1149 [exclusions] 1 2 3 2 1 3 3 1 2 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
