[gmx-users] how to make a rigid entity
I would like to calculate the PMF between two nanotubes covered with surfactants. for doing this, one nanotube have to hold fixedly and another one have to move as rigid entity. for fixed nanotube I used position restraints, however, I do not know how to make a nanotube a rigid entity? I would be pleased if someone could help me. Thank you -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] how to remove some molecules
Dear gmx-users I would like to calculate the PMF in a system composed of nanotube+surfactants. for doing this I use the final configuration of previous surfactant adsorption simulation onto carbon nanotube. the problem is I want to remove some of non-adsorbed surfactant molecules. Would you please help me how I can do that? any help would be highly appreciated. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] how to remove some molecules
Thank you Sir for your reply. but I do not know how to recognize the non-adsorbed molecules in a gro file? Is there any way to recognize them in a gro file( I have seen the in VMD)? -- 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] (no subject)
Dear gmx users I am analyzing simulation results of a system including carbon nanotube+surfactant molecules. I would like to calculate the number of surfactants located on a specific distance(say 1 nm ) from nanotube in each timestep or average of that quantity.I would be really appreciated if someone could help to calculate that?is there any program in gromacs to do that? Best regards -- 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] calculation of angle between two groups
Dear gmx users I did the simulations of carbon nanotube+surfactant+water molecules and I would like to calculate probability distribution of the angle formed between the vector of the surfactant molecules and CNT. Is there any tools or programs in gromacs to do that?I have tried g_sgangle program but it gave me the error.any suggestion would be highly appreciated. Best regards -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] calculation of angle between two groups
Dear Mark thank you for your concern.when I tried the g_sgangle program it gave me Fatal error: Something wrong with contents of index file. the index file was the one I used during the simulation and I made that with this command: make_ndx -f em.gro -o index.ndx and the groups for temperature couplig was tc-grps= MOL_LIG Water_and_ions it means that I coupled carbon nanotube(MOL) and surfacatnt(LIG) together. I would be really pleased if you could help me. Best regards -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] segmentation fault during equilibration
Dear gmx users, I am simulating a system including carbon nanotube(a finite one)+water+surfactant and so far I have done these things: 1.I generated the topology of CNT ( opls force field) by this command: g_x2top -f cnt.pdf -o cnt.top -nopairs -nexcl 3 -name CNT 2.I used TopolGen to produce topology of surfactant and I calculated the charges of atomes by the RESP method and checked the atomtypes to make sure that they make sence as well.so I changed some atomtypes according to the opls. 3.I build a topol.top file that contains topolgy of CNT+surfactant. 4.I created the initial configuration for the CNT+surfactant by means of packmol. 5.I used editconf and genbox with these command: editconf -f CNTSUR.pdb -o newbox.gro -d 0.7 -bt cubic genbox -cp newbox.gro -cs spc216.gro -p topol.top -o solv.gro 6.I run grompp and genion for adding the ions: grompp -f em.mdp -c solv.gro -p topol.top -o ions.tpr genion -s ions.tpr -p topol.top -o solv_ions.gro -nname BR -nn 28 7.I run grompp again for energy minimization: grompp -f em_real.mdp -c solv_ions.gro -p topol.top -o em.tpr mdrun -deffnm em the em_real.mdp file contains: ; 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 10.0 kJ/mol emstep = 0.01 ; Energy step size nsteps = 7 ; Maximum number of (minimization) steps to perform energygrps = UNK LIG ; Which energy group(s) to write to disk ; 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 = 0.9 ; Cut-off for making neighbor list (short range forces) coulombtype = PME ; Treatment of long range electrostatic interactions rcoulomb= 0.9 ; long range electrostatic cut-off rvdw= 1.4 ; Periodic Boundary Conditions (yes/no) pbc = xyz ; Periodic Boundary Conditions (yes/no) 8.then I made an index file for CNT and surfactant and used genrestr to restraint the CNT and surfactant during equilibration. 9.I run grompp and mdrun with these command:grompp -f nvt.mdp -c em.gro -p topol.top -o nvt.tpr -n index.ndx mdrun -deffnm nvt and after passing 42900 of 5 steps, segmentation fault occured.I checked the log file but it did not contain any errors and I also used VMD to see trajetory but I did not see anything wrong. I would be pleased if anyone could help me how to fix this. -- 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] segmentation fault during equilibration
thank you Sir for your reply.below I provide you .mdp file: title = UNK-ligand complex NVT equilibration define = -DPOSRES -DPOSRES_LIG ; position restrain the UNK and LIG ; Run parameters integrator = md; leap-frog integrator nsteps = 5; 2 * 5 = 100 ps dt = 0.002 ; 2 fs ; Output control nstxout = 1 ; save coordinates every 0.2 ps nstvout = 1 ; save velocities every 0.2 ps nstenergy = 100 ; save energies every 0.2 ps nstlog = 100 ; update log file every 0.2 ps energygrps = UNK LIG ; Bond parameters continuation= no; first dynamics run constraint_algorithm = lincs; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighborsearching ns_type = grid ; search neighboring grid cells nstlist = 5 ; 10 fs rlist = 0.9 ; short-range neighborlist cutoff (in nm) rcoulomb= 0.9 ; short-range electrostatic cutoff (in nm) rvdw = 1.4 ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling is on tcoupl= V-rescale ; modified Berendsen thermostat tc-grps = UNK_LIG Water_and_ions; two coupling groups - more accurate tau_t = 0.1 0.1 ; time constant, in ps ref_t = 300 300 ; Pressure coupling is off pcoupl = no; no pressure coupling in NVT ; Periodic boundary conditions pbc= xyz ; 3-D PBC ; Dispersion correction DispCorr= EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = yes ; assign velocities from Maxwell distribution gen_temp= 300 ; temperature for Maxwell distribution gen_seed= -1; generate a random seed -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: gmx-users Digest, Vol 97, Issue 6
Dear Justin the results of EM was: Steepest Descents converged to Fmax 1000 in 77 steps Potential Energy = -3.6802272e+05 Maximum force = 8.9652832e+02 on atom 1556 Norm of force = 1.1512711e+02 thank you for your concern On Tue, May 1, 2012 at 9:33 PM, gmx-users-requ...@gromacs.org wrote: Send gmx-users mailing list submissions to gmx-users@gromacs.org To subscribe or unsubscribe via the World Wide Web, visit http://lists.gromacs.org/mailman/listinfo/gmx-users or, via email, send a message with subject or body 'help' to gmx-users-requ...@gromacs.org You can reach the person managing the list at gmx-users-ow...@gromacs.org When replying, please edit your Subject line so it is more specific than Re: Contents of gmx-users digest... Today's Topics: 1. Re: POPC: ff53a6 and CHARMM36 formats (Justin A. Lemkul) 2. Re: segmentation fault during equilibration (Justin A. Lemkul) 3. Re: minimum distance between periodic images does not aggree with box dimensions (Tsjerk Wassenaar) 4. saltbridges newbie question (Denis Kazakiewicz) 5. Re: disre and posres together? (Mark Abraham) 6. Re: saltbridges newbie question (Peter C. Lai) 7. Re: saltbridges newbie question (Denis Kazakiewicz) -- Message: 1 Date: Tue, 01 May 2012 08:16:14 -0400 From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] POPC: ff53a6 and CHARMM36 formats To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4f9fd40e.5070...@vt.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed On 5/1/12 8:05 AM, Ángel Piñeiro wrote: I guess there are better solutions but an alternative is to map your bilayer to MARTINI (http://md.chem.rug.nl/cgmartini/) and then to use SUGAR-PIE (http://smmb.usc.es/sugarpie/sugarpie.php) to go to from MARTINI to all-atom CHARMM36. Even simpler would be to fix the offending atom names and build a suitable .hdb entry (if one does not already exist) and produce the topology with pdb2gmx. I would think it would then be far easier to preserve the original configurations of the lipids, rather than changing the resolution back and forth. -Justin Hope it helps, Ángel. On Tue, 2012-05-01 at 17:25 +0530, Anirban Ghosh wrote: Hi ALL, I have a equilibrated POPC bilayer (100 ns run) that I have run using GROMOS ff53a6 FF. Now, I wish to use this POPC bilayer for a new simulation using CHARMM36 FF in GROAMCS 4.5.5. There are differences in atom naming conventions (N, P, C, O) between this two FFs as a result of which pdb2gmx gives error. Can these atom names (hydrogens can be ignored) of my equilibrated POPC bilayer be changed manually and then used with CHARMM36 FF? Thanks a lot in advance. Regards, Anirban -- gmx-users mailing listgmx-us...@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive athttp://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 togmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Readhttp://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 -- Message: 2 Date: Tue, 01 May 2012 08:42:26 -0400 From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] segmentation fault during equilibration To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4f9fda32.6010...@vt.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed On 5/1/12 7:19 AM, niaz poorgholami wrote: Dear gmx users, I am simulating a system including carbon nanotube(a finite one)+water+surfactant and so far I have done these things: 1.I generated the topology of CNT ( opls force field) by this command: g_x2top -f cnt.pdf -o cnt.top -nopairs -nexcl 3 -name CNT 2.I used TopolGen to produce topology of surfactant and I calculated the charges of atomes by the RESP method and checked the atomtypes to make sure that they make sence as well.so I changed some atomtypes according to the opls. 3.I build a topol.top file that contains topolgy of CNT+surfactant. 4.I created the initial configuration for the CNT+surfactant by means of packmol. 5.I used editconf and genbox with these command: editconf -f CNTSUR.pdb -o newbox.gro -d 0.7 -bt cubic Unrelated to the crash, but if your longest cutoff is 1.4 nm, setting a solute-box distance of 0.7 nm will lead to trouble if you ever use NPT. With just a small fluctuation
[gmx-users] segmentation fault during equilibration
Dear Justin the results of EM was: Steepest Descents converged to Fmax 1000 in 77 steps Potential Energy = -3.6802272e+05 Maximum force = 8.9652832e+02 on atom 1556 Norm of force = 1.1512711e+02 thank you for your concern -- 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] add nonbonded parameter for interaction between CNT and waters
Dear all I am simulating carbon nanotube in water and I would like to use Lennard-Jones potential For interaction between carbon nanotube and waters with these parameters: σco =3.19˚ A εco =0.392 kJ/mol I know that I should add these parameters manually in ffnonbonded.itp however, I have no Idea where and how can I do that in the ffnonbonded.itp. Any help would be appreciated. -- 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] rigid carbon nanotube
Dear All I would be pleased if anyone could tell me how to kept a carbon nantube rigid throughout the simulations ? thank you -- 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] grompp error for CNT+surfactant simulation
Dear all I am using Gromacs 4.5.3 to simulate a system including: CNT+water+surfactant and I want to use opls force field for my whole system. so far I have done following things: 1.I copied oplsaa.ff folder in my working directory. 2.I added following lines to atomname2type.n2t Copls_9950 12.011 1C 0.142 Copls_9960 12.011 2C 0.142 C 0.142 Copls_9970 12.011 3C 0.142 C 0.142 C 0.142 Copls_9980 12.011 4C 0.142 C 0.142 C 0.142 C 0.142 3.I added these to ffbonded.itp [ bondtypes ] C C 1 0.14210 478900 [ angletypes ] C C C 1 120.000 397.480 [ dihedraltypes ] C C 1 0.000 167.360 1 4.I added these to ffnonbonded.itp opls_995 C 612.01100 0.000 A3.851000e-01 4.39600e-01 opls_996 C 612.01100 0.000 A3.851000e-01 4.39600e-01 opls_997 C 612.01100 0.000 A3.851000e-01 4.39600e-01 opls_998 C 612.01100 0.000 A3.851000e-01 4.39600e-01 5.I used g_x2top to create topology for CNT. Command line was: g_x2top -f cnt.pdb -o cnt.top -r cnt.rtp -name CNT -nexcl 5 6.I used TopolGen to produce the *.itp file for surfactant molecule. 7.I placed surfactant molecules around CNT. 8.I used editconf using this command: editconf -f cnt_sur.pdb -o cnt_sur.gro -c -d 1 -bt cubic 9. I wrote a a .top file given below, Include forcefield parameters #include ./oplsaa.ff/forcefield.itp ; Include topology for DTAB #include DTAB.itp ; Include topology for CNT #include cnt.itp ; [ molecules ] ; molecule name nr. DTAB 14 CNT 1 10.I called genbox with the command: genbox -cp cnt_sur.gro -cs spc216.gro -p topol.top -o solv.gro 11.I added manually these to topol.top ; Include SPC water topology #include oplsaa.ff/spc.itp 12. once I run grompp : grompp -f em.mdp -c solv.gro -p topol.top -o ions.tpr I got following errors: Ignoring obsolete mdp entry 'title' WARNING 1 [file ffbonded.itp, line 2704]: Overriding Bond parameters. old: 0.151 292880 0.151 292880 new: C C 1 0.14210 478900 Generated 335790 of the 335790 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 335790 of the 335790 1-4 parameter combinations ERROR 1 [file DTAB.itp, line 104]: No default Bond types ERROR 2 [file DTAB.itp, line 105]: No default Bond types ERROR 3 [file DTAB.itp, line 241]: No default Angle types ERROR 4 [file DTAB.itp, line 242]: No default Angle types ERROR 5 [file DTAB.itp, line 244]: No default Angle types ERROR 6 [file DTAB.itp, line 245]: No default Angle types ERROR 7 [file DTAB.itp, line 249]: No default Angle types ERROR 8 [file DTAB.itp, line 302]: No default Ryckaert-Bell. types ERROR 9 [file DTAB.itp, line 303]: No default Ryckaert-Bell. types Excluding 3 bonded neighbours molecule type 'DTAB' Excluding 5 bonded neighbours molecule type 'CNT' Excluding 2 bonded neighbours molecule type 'SOL' NOTE 1 [file topol.top, line 27]: System has non-zero total charge: 5.03e+00 There was 1 note There was 1 warning --- Program grompp, VERSION 4.5.3 Source code file: /build/buildd/gromacs-4.5.3/src/kernel/grompp.c, line: 1356 Fatal error: There were 9 errors in input file(s) --- I would be more than pleased if someone could guild me how to solve the problem. -- 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] grompp error for CNT simulation
Dear gmx users, I am using gromacs 4.5.3 to simulate CNT in water. up to now I have done these things: 1. I used packmol to create my PDB file and the used editconf to change PDB to gro file. 2. I copied oplsaa.ff folder in my working directory 3. I added following lines to atomname2type.n2t Copls_9950 12.011 2C 0.142 C 0.142 Copls_9960 12.011 3C 0.142 C 0.142 C 0.142 Copls_9970 12.011 4C 0.142 C 0.142 C 0.142 C 0.142 Copls_9980 12.011 5C 0.142 C 0.142 C 0.142 C 0.142 C 0.142 4. I added these to atomtypes.atp opls_995 12.01100 opls_996 12.01100 opls_997 12.01100 opls_998 12.01100 5. I added these to ffbonded.itp [ bondtypes ] C C 1 0.14210 478900 [ angletypes ] C C C 1 120.000 397.480 [ dihedraltypes ] C C 1 0.000 167.360 1 6. I used g_x2top to create topology for CNT. Command line was: g_x2top -f CNT.gro -o CNT.top -pbc -nopairs -name CNT -nexcl 5 7. I wrote a .top file given below, ; Include forcefield parameters #include ./oplsaa.ff/forcefield.itp ; Include topology for water #include oplsaa.ff/spc.itp ; Include topology for CNT #include oplsaa.ff/CNT.itp [ system ] ; Name SDS and CNT in water [ molecules ] ; Compound#mols water 9000 CNT 1 8. when I run grompp for EM with this command line :grompp -f md.mdp -c cnt_alone.gro -p topol.top -o em.tpr it gave me the following error:Atomtype opls_995 not found. I would be pleased if anyone could help me how to fix this. niaz -- 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
