Re: [gmx-users] coenzyme-protein complex
Dear Justin My final .xtc rmsd graph starts about 4 nm and after some steps it falls down to 0.3 and quickly goes up again, totally it is tossing around a straight line near 4 nm, what did I do wrong? As mentioned in my previous mail about centering of protein inside the box, the gro file was attached. The rmsd graph and gro files are uploaded at the following links: gro link: https://www.hightail.com/download/elNKUXVzTkw1bmo1SE1UQw xvg link: https://www.hightail.com/download/elNKUXVzTkxtMEpYd3NUQw * I run nvt for 5 and npt for 5 then mdrun for 5ns the md.mdp file is title = Protein-ligand complex MD simulation ; Run parameters integrator = md; leap-frog integrator nsteps = 500; 2 * 500 = 1000 ps (10 ns) dt = 0.002 ; 2 fs ; Output control nstxout = 0 ; suppress .trr output nstvout = 0 ; suppress .trr output nstenergy = 1000 ; save energies every 2 ps nstlog = 1000 ; update log file every 2 ps nstxtcout = 1000 ; write .xtc trajectory every 2 ps energygrps = Protein LIG ; Bond parameters continuation= yes ; 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 = 1.2 ; short-range neighborlist cutoff (in nm) rlistlong = 1.4 rcoulomb= 1.2 ; short-range electrostatic cutoff (in nm) rvdw= 1.2 ; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation vdwtype = switch rvdw_switch = 0.8 fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling tcoupl = V-rescale ; modified Berendsen thermostat tc-grps = Protein_MG_LIG Water_and_ions ; two coupling groups - more accurate tau_t = 0.1 0.1 ; time constant, in ps ref_t = 310 310 ; reference temperature, one for each group, in K ; Pressure coupling pcoupl = Parrinello-Rahman ; pressure coupling is on for NPT pcoupltype = isotropic ; uniform scaling of box vectors tau_p = 2.0 ; time constant, in ps ref_p = 1.0 ; reference pressure, in bar compressibility = 4.4e-5; isothermal compressibility of water, bar^-1 ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr= EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = no; assign velocities from Maxwell distribution * Sincerely M.Javaheri On Sat, 02/01/2014 04:17 AM, Justin Lemkul jalem...@vt.edu wrote: On 1/31/14, 11:53 AM, Mostafa Javaheri wrote: Dear Justin I have a problem with centering the hetrodimer protein in the dodecahedron or octahedron box, the related commands are: 1.pdb2gmx -f A1CBIII-W3.pdb -ff charmm27 -water tip3p -ignh -o conf.pdb -nochargegrp -merge all -posrefc 1000 -renum 2.editconf -f conf.pdb -o boxed.pdb -c -d 1.0 -bt dodecahedron 3.genbox -cs -cp boxed.pdb -o solvated.pdb -p topol.top in the solvated.pdb output file protein represents at the corner of the box and some of it is out of box although it will not happen for -bt cubic (whole protein will be centered in the box), considering periodic boundary condition, mdrun will be ok; after five ns mdrun one of the protein's chain represents inside the box and the other chain out of the box in md.gro file. After running trjcov several times with different options (including -pbc mol, atom, nojump, whole -center, -ur compact) none of them could put the whole protein in one unit cell. I would be grateful again for your help. Without seeing exactly what you've tried, it's rather futile to try to guess what to suggest. Complexes are difficult to deal with. The first step should almost always be trjconv -pbc nojump, but further iterations may vary. See http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions#Suggested_trjconv_workflow and also be aware that you can (and should, in many cases) use custom index groups for centering or other fitting, i.e. some residues at the protein-protein interface or something else that makes sense. Centering on protein normally fails in such cases, for reasons discussed repeatedly in the list archive. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow
[gmx-users] pbc problem
Dear Justin and Tsjerk you said Some tools handle PBC properly, some don't . I want to know exactly which tools of gromacs handle PBC properly. Can I find these tools in manual? I did simulation of a system containing protein and cnt using gromacs 4.5.6. When I see trajectory by VMD, in some frames, protein atoms exit one side of box and enter opposite side of box. I want to do analysis of trajectory. I do not know exactly this state is pbc problem or not. Any help will 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.
Re: [gmx-users] pbc problem
On 2/2/14, 7:15 AM, Atila Petrosian wrote: Dear Justin and Tsjerk you said Some tools handle PBC properly, some don't . I want to know exactly which tools of gromacs handle PBC properly. Can I find these tools in manual? No, because it's not possible to test every single command that the user might issue and keep a reliable database of such information. I did simulation of a system containing protein and cnt using gromacs 4.5.6. When I see trajectory by VMD, in some frames, protein atoms exit one side of box and enter opposite side of box. I want to do analysis of trajectory. I do not know exactly this state is pbc problem or not. Again, that depends entirely upon the command you're using. Tools like g_rms have problems when molecules are split across PBC. Other tools like g_dist or g_msd handle the situation better. If the protein is the only problematic molecule, it should be rather trivial to fix the PBC issues with trjconv -center, trjconv -pbc nojump, trjconv -pbc mol -ur compact, or trjconv -fit translation, or perhaps some sequence of those. Please refer to the PBC link I have posted several times this week. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 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.
[gmx-users] Bond interaction exclusions
Dear all, I am unclear about the bond exclusion properties within gromacs. Using a martini model system, what is the default behavior of setting [moleculetype] ;name exclusions eth 1 exclusions to 1? How do I find out what kind of interaction it is excluding? I am interested in finding out if this is excluding 1-3 interaction or 1-4 interaction. I guess what I also want to know is if my settings are including 1-4 bonded interactions or using only 1-3. Please let me know, 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] Bond interaction exclusions
On 2/2/14, 11:29 AM, Xu Dong Huang wrote: Dear all, I am unclear about the bond exclusion properties within gromacs. Using a martini model system, what is the default behavior of setting [moleculetype] ;name exclusions eth 1 exclusions to 1? How do I find out what kind of interaction it is excluding? I am interested in finding out if this is excluding 1-3 interaction or 1-4 interaction. I guess what I also want to know is if my settings are including 1-4 bonded interactions or using only 1-3. The value of nrexcl is the number of bonded neighbors that are excluded from nonbonded interactions. With nrexcl = 1, only 1-2 interactions are excluded; 1-3 and 1-4 interactions are calculated as normal nonbonded interactions. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 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] Bond interaction exclusions
Hi, The first line eth1 tells it all. In that molecule all non-bonded interactions between first bonded neighbors will be excluded. Thus the 1-3, 1-4 (and so on) non-bonded interactions will be included. You may add additional exclusions in the [ exclusion ] section of your topology. I am not sure what you mean with 1-4 bonded interactions but if you mean non-bonded then see above. On Feb 2, 2014, at 17:29, Xu Dong Huang xudonghm...@gmail.com wrote: Dear all, I am unclear about the bond exclusion properties within gromacs. Using a martini model system, what is the default behavior of setting [moleculetype] ;nameexclusions eth 1 exclusions to 1? How do I find out what kind of interaction it is excluding? I am interested in finding out if this is excluding 1-3 interaction or 1-4 interaction. I guess what I also want to know is if my settings are including 1-4 bonded interactions or using only 1-3. Please let me know, 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] codes for non-bonded function selection (NBF)
Hi,
As you can see in the comment at the top of that file, you will need to
make matching changes to some arrays in src/gmxlib/names.c
Mark
On Sat, Feb 1, 2014 at 3:11 AM, Makoto Yoneya makoto-yon...@aist.go.jpwrote:
Dear Gromacs exparts:
I'd like to add the non-boded function selection (NBF) corresponds to
a truncated LJ potential known as
Weeks-Chandler-Andersen (WCA) potential.
I'd post this in the past and I'd suceeded to calculate that with th hard
code
modifications.
Now, I'd like to make selection switch for this new NBF selection.
I'd tried to modify the include/types/enums.h NBFselection line from
enum {
eNBF_NONE, eNBF_LJ, eNBF_BHAM, eNBF_NR
};
to
enum {
eNBF_NONE, eNBF_LJ, eNBF_BHAM,eNBF_WCA, eNBF_NR
};
. i.e., simply add a new selection (eNBF_WCA) and shift eNBF_NR.
However, only this modification resulted in secgentation error in
grompp execution.
Does anone know how to add a new NBF selection correctly?
Thank you for advance.
Makoto Yoneya, Dr.
AIST, Tsukuba
JAPAN
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Re: [gmx-users] Bond interaction exclusions
On Sun, Feb 2, 2014 at 5:29 PM, Xu Dong Huang xudonghm...@gmail.com wrote: Dear all, I am unclear about the bond exclusion properties within gromacs. Using a martini model system, what is the default behavior of setting [moleculetype] ;name exclusions eth 1 exclusions to 1? The others have covered this one How do I find out what kind of interaction it is excluding? grompp will produce slightly different output to the terminal, but this is not really what you want. I am interested in finding out if this is excluding 1-3 interaction or 1-4 interaction. I guess what I also want to know is if my settings are including 1-4 bonded interactions or using only 1-3. Only by inspecting the contents of the .tpr can you really know what is going on. You can compare two .tpr files with gmxcheck, but for your own sanity, I would construct a very simple input file (e.g. ethane) before attempting this. Mark Please let me know, 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] simulating multiple molecules in a box
On Sun, Feb 2, 2014 at 8:28 PM, ibrahim khalil ibrahim.khalil.c...@gmail.com wrote: hi, i am new to gromacs. i was trying simulate multiple (eg. 3 or 4 ) carbon nanotubes in a single box. The way I am trying to do is ... 1. Take both pdb files, merge them(using pymol) according to my orientation and create a single pdb file for the whole structure. 2. Generate the gro and hence the topology file using the forecfield I used to simulate a single cnt. 3. Run the mdrun program. I was wondering if there is anything wrong with this procedure. (I saw the posts for simulating multiple proteins in a single box and found it suggests simulating different proteins separately and then creating their topology files, converting them into .itp and then running the simulation) For grompp, you need a topology that matches your input coordinates. How to generate each depends very much on the contents of the system, because different tools are available for proteins vs things like nanotubes. Those posts were probably referring to using pdb2gmx to generate topologies for each protein that could then be merged. You may not have that problem. Also I am having some problems with the bonds. Whenever the CNTs are a little bit close[not too close to create a bond in between them], some unwanted bonds between two CNTs are created. it would be very nice if anyone could help me solve this problem. Maybe it's not a problem. See http://www.gromacs.org/Downloads/Related_Software/Visualization_Software#Topology_bonds_vs_Rendered_bonds Mark Thanks for your time. -- View this message in context: http://gromacs.5086.x6.nabble.com/simulating-multiple-molecules-in-a-box-tp5014224.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] Simulating spherocylinders
No. Mark On Sun, Feb 2, 2014 at 7:25 PM, Sanku M msank...@yahoo.com wrote: Dear Gromacs users Is it possible to simulate md of rigid spherocylinders in grimaces? Thanks Sanku -- 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] Replica Exchange MD
Dear GMX Users, I am trying to apply the REMD to study the difference between the folding free energy of a 24 residue peptide with two different conformations. As I am short of required number of processors for REMD in explicit water, I am trying my luck with implicit solvent. I have come across many papers that have used implicit solvent in their simulation studies. So, after various trails of temp. distributions, I selected some 15 replicas with the following temp. range: Repl 0 1 2 3 4 5 6 7 8 910 11121314 Repl T 250.0 264.0 279.0 295.0 312.0 329.0 348.0 367.0 388.0 410.0 433.0 458.0 484.0 511.0 540.0 Repl Repl exchange interval: 1000 Here's the result for a trial run of 2ns per replica: Replica exchange statistics Repl 999 attempts, 500 odd, 499 even Repl average probabilities: Repl 0123456789 10 11 12 13 14 Repl .34 .34 .21 .27 .39 .41 .40 .37 .41 .42 .41 .43 .46 .44 Repl number of exchanges: Repl 0123456789 10 11 12 13 14 Repl 166 155 116 130 184 201 193 185 212 216 200 208 223 225 Repl average number of exchanges: Repl 0123456789 10 11 12 13 14 Repl .33 .31 .23 .26 .37 .40 .39 .37 .42 .43 .40 .42 .45 .45 The average exchange ratio for each replica lies between 0.3-0.4. Is it okay ? . As the value between 0.2-0.3 is considered to be good. Here's the graph for replica_index , replica_temp and PE of replicas. https://www.dropbox.com/s/dykxwwqulpfpw8x/REMD.png I want to know whether, I can move forward with the large production runs or not ?? Pls respond - Bharat -- 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.
