Re: [gmx-users] atoms are not part of any of the T-Coupling groups
gmxcheck of my index file gives: Contents of index file index.ndx -- Nr. Group #Entries FirstLast 0 System 2230 12230 1 Protein 2226 12226 2 Protein-H 2226 12226 3 C-alpha 308 32218 4 Backbone 922 12219 5 MainChain 1232 12226 6 MainChain+Cb1488 12226 7 MainChain+H 1232 12226 8 SideChain994 82225 9 SideChain-H 994 82225 10 Prot-Masses 2226 12226 11 non-Protein422272230 12 Ion422272230 13 CU 222272229 14 ZN 222282230 15 r_131__chA8 956 963 16 r_131__chB820692076 17 r_132 1112071217 18 r_286 1126112621 19 CA_chA_r131112091209 20 CA_chB_r131126132613 and following are the contents of my .mdp file: title = Umbrella pulling simulation define = -DPOSRES_CA_chA_r131 ; Run parameters integrator = md dt = 0.002 tinit = 0 nsteps = 25; 500 ps nstcomm = 10 ; Output parameters nstxout = 5000 ; every 10 ps nstvout = 5000 nstfout = 500 nstxtcout = 500 ; every 1 ps nstenergy = 500 ; Bond parameters constraint_algorithm= lincs constraints = all-bonds continuation= yes ; continuing from NPT ; Single-range cutoff scheme nstlist = 5 ns_type = grid rlist = 1.4 rcoulomb= 1.4 rvdw= 1.4 ; PME electrostatics parameters coulombtype = PME fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft= yes ; Berendsen temperature coupling is on in two groups Tcoupl = Nose-Hoover tc_grps = Protein Non-Protein tau_t = 0.5 0.5 ref_t = 310 310 ; Pressure coupling is on Pcoupl = Parrinello-Rahman pcoupltype = isotropic tau_p = 1.0 compressibility = 4.5e-5 ref_p = 1.0 refcoord_scaling = com ; Generate velocities is off gen_vel = no ; Periodic boundary conditions are on in all directions pbc = xyz ; Long-range dispersion correction DispCorr= EnerPres ; Pull code pull= umbrella pull_geometry = distance ; simple distance increase pull_dim= Y N N pull_start = yes ; define initial COM distance 0 pull_ngroups= 1 pull_group0 = CA_chA_r131 pull_group1 = CA_chB_r131 pull_rate1 = 0.01 ; 0.01 nm per ps = 10 nm per ns pull_k1 = 4200 ; kJ mol^-1 nm^-2 Thanks in advance. Nidhi On Wed, Aug 6, 2014 at 8:06 PM, Justin Lemkul jalem...@vt.edu wrote: On 8/6/14, 3:46 AM, Nidhi Katyal wrote: Hello all, I am working on protein with two chains. I would like to restrain one atom of one chain while doing steered MD. For the same reason, I have created an index file that includes that atom, then created its posre.itp file and finally included following lines at the end of topol_Protein_chainA.itp: ; Include Position restraint file #ifdef POSRES_CA_chA_r131 #include posre.itp #endif I am also pasting a small section of my topol.top file: ; Include forcefield parameters #include gromos53a6.ff/forcefield.itp ; Include chain topologies #include topol_Protein_chain_A.itp #include topol_Protein_chain_B.itp #include topol_Ion_chain_A2.itp #include topol_Ion_chain_B2.itp ; Include water topology #include gromos53a6.ff/spc.itp #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif After carrying out NPT equilibration, when I run following command: grompp -f md_pull.mdp -c npt.gro -p topol.top -n index.ndx -t npt.cpt -o pull.tpr as given in tutorial: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ gmx-tutorials/umbrella/05_pull.html I am getting following error: 215400 atoms are not part of any of the T-Coupling groups Since my pull.mdp file as the same as given in tutorial, my coupling groups are Protein and Non-Protein. I suspect there is something wrong while adding restraints using include file mechanism. Please help me resolve the problem. The error is not a result of the #include mechanism; it's a problem in the group definitions, either in the .mdp file or in the index file. Without the full text of the .mdp and the gmxcheck output of the index.ndx file, there's little to suggest. -Justin --
[gmx-users] Spherical Averaging (Debye formulation) in SAXS calculation!
Dear all, Anyone calculated SAXS profile using gmx saxs option. It is under g_rdf for gromacs 4.6.x version. My question is whether the spherical averaging has been implemented in this tool. I have checked the program, it seems spherical averaging is not implemented. Moreover, orientation of the solute molecule has effect on the SAXS profile calculated with this tool. For SANS calculation(g_sans), debye formulation is used to incorporate the spherical averaging. Why different methodology is adopted in SAXS and SANS calculation. Any clarification is greatly appreciated. Thanks in Advance. -- 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] Gromacs 5.0 installation
Hi everyone, I'm trying to install Gromacs 5.0 on a computer which has no network connection. It would be appreciated if some one tell me how this can be done! Regards Fatemeh -- 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] How to profile GMX?
Hi, I would like to know what kind of profiling tools can be used with GMX? Which is the most commonly used one? -- 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] how to write in a script?
Dear Albert,
You can have a look at the following page
http://www.gromacs.org/Documentation/How-tos/Using_Commands_in_Scripts
Chandan
On Thu, Aug 7, 2014 at 4:29 PM, Albert mailmd2...@gmail.com wrote:
Hello:
I am trying to make a workflow of system building steps of gromacs.
However, many steps require interactive input such as:
genion, make_ndx
the genion can be done with echo:
echo 15| ${genion} -s Complex_b4ion.tpr
However, when I try to run:
echo 1|14 make_ndx -f input.pdb
However, it doesn't work for the above command.
Does anybody have any idea how can we write make_ndx in a script?
thx a lot
Albert
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Re: [gmx-users] how to write in a script?
Hi Chanda: thx a lot for the helps, it works now. However, I've got another question: I am trying to insert #ifdef POSRES_UNK into ligand.itp file between fowllowing two lines: ; position restraints for System of [ position_restraints ] Here is my script: cat $pwd/$i/tmp.itp | sed '/; position restraints for System of \/a\ #ifdef POSRES_UNK ' | tmp2.itp cat tmp2.itp ligand.itp But it seems that the string #ifdef POSRES_UNK doesn't add to desired .itp file. Does anybody have any idea where is the problem? thx a lot Albert On 08/07/2014 01:04 PM, Chandan Choudhury wrote: Dear Albert, You can have a look at the following page http://www.gromacs.org/Documentation/How-tos/Using_Commands_in_Scripts Chandan -- 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] What files should I delete after simulation?
Dear Users, I have subsequent simulations of MD. I need to delete some unimportant files for analyses. What files should I delete? Best regards, Batsaikhan -- 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] how to write in a script?
Something like this. Edit it according to your needs. cat file EOF #ifdef POSRES_UNK EOF Yay! Cheers, /J On Thu, Aug 7, 2014 at 12:50 PM, Albert mailmd2...@gmail.com wrote: Hi Chanda: thx a lot for the helps, it works now. However, I've got another question: I am trying to insert #ifdef POSRES_UNK into ligand.itp file between fowllowing two lines: ; position restraints for System of [ position_restraints ] Here is my script: cat $pwd/$i/tmp.itp | sed '/; position restraints for System of \/a\ #ifdef POSRES_UNK ' | tmp2.itp cat tmp2.itp ligand.itp But it seems that the string #ifdef POSRES_UNK doesn't add to desired .itp file. Does anybody have any idea where is the problem? thx a lot Albert On 08/07/2014 01:04 PM, Chandan Choudhury wrote: Dear Albert, You can have a look at the following page http://www.gromacs.org/Documentation/How-tos/Using_Commands_in_Scripts Chandan -- 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] how to write in a script?
Hi Joao: thanks a lot for kind reply. I don't get the point how to use it properly. I am trying to insert #ifdef POSRES_UNK betwee the following two lines: ; position restraints for System of [ position_restraints ] It should be looks like the following after script: ; position restraints for System of #ifdef POSRES_UNK [ position_restraints ] can you elaberate more how to use it? I tried to run it with command: cat tmp.itp ligand.itp EOF ? #ifdef POSRES_UNK ? EOF it seems doesn't work... THX Albert On 08/07/2014 02:37 PM, João Henriques wrote: Something like this. Edit it according to your needs. cat file EOF #ifdef POSRES_UNK EOF -- 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] can we use Area per lipid: 1.00 nm^2
Hello All I am trying to perform MD for protein-ligand complex in popc lipid with Charmm36 force field and also follow Justin A. Lemkul tutorial. I performed perl inflategro.pl system.gro 4 POPC 0 system_inflated.pdb 5 area.dat followed by energy minimization then, perl inflategro.pl em.gro 0.95 POPC 0 system_shrink1.gro 5 area_shrink1.dat followed by energy minimization then after 16 iteration of scaling down by 0.95 I got Area per lipid: 1.00 nm^2. In 17th iteration Area per lipid become 0.80 nm^2. but after that when I visualize the .gro file i.e system_shrink17.gro the ligand molecule is far from protein and out of lipid. But till 16th iteration its inside the lipid in its normal position. Should I perform till 16th iteration which gives area per lipid 1.00 nm^2 ? Is it a good value for Area per lipid ?? or there is some error in my files. My topology file is : ; Include forcefield parameters #include charmm36_lipid.ff/forcefield.itp ; Include Position restraint file #ifdef POSRES #include posre.itp #endif ; Include ligand topology #include LIG.itp ; Ligand position restraints #ifdef POSRES #include posre_LIG.itp #endif [ moleculetype ] ; Namenrexcl Protein 3 [ atoms ] . . . . . . ; Strong position restraints for InflateGRO #ifdef POSRES_STRONG #include strong_posre.itp #endif ; Include POPC chain topology #include popc.itp ; Include water topology #include charmm36_lipid.ff/tip3p.itp #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ; Include topology for ions #include charmm36_lipid.ff/ions.itp [ system ] ; Name Gyas ROwers Mature At Cryogenic Speed [ molecules ] ; Compound#mols Protein 1 LIG 1 POPC 128 Please Help Thank you very much. With Regards Neha bharty -- 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] atoms are not part of any of the T-Coupling groups
On 8/7/14, 12:16 AM, Nidhi Katyal wrote: gmxcheck of my index file gives: It looks like you have created the index file before adding any solvent. Hence you have 215000+ atoms that are not accounted for. You need to generate index files after the system is complete. You can, of course, re-use your custom groups, but they need to be used in addition to sensible groups for everything else. -Justin Contents of index file index.ndx -- Nr. Group #Entries FirstLast 0 System 2230 12230 1 Protein 2226 12226 2 Protein-H 2226 12226 3 C-alpha 308 32218 4 Backbone 922 12219 5 MainChain 1232 12226 6 MainChain+Cb1488 12226 7 MainChain+H 1232 12226 8 SideChain994 82225 9 SideChain-H 994 82225 10 Prot-Masses 2226 12226 11 non-Protein422272230 12 Ion422272230 13 CU 222272229 14 ZN 222282230 15 r_131__chA8 956 963 16 r_131__chB820692076 17 r_132 1112071217 18 r_286 1126112621 19 CA_chA_r131112091209 20 CA_chB_r131126132613 and following are the contents of my .mdp file: title = Umbrella pulling simulation define = -DPOSRES_CA_chA_r131 ; Run parameters integrator = md dt = 0.002 tinit = 0 nsteps = 25; 500 ps nstcomm = 10 ; Output parameters nstxout = 5000 ; every 10 ps nstvout = 5000 nstfout = 500 nstxtcout = 500 ; every 1 ps nstenergy = 500 ; Bond parameters constraint_algorithm= lincs constraints = all-bonds continuation= yes ; continuing from NPT ; Single-range cutoff scheme nstlist = 5 ns_type = grid rlist = 1.4 rcoulomb= 1.4 rvdw= 1.4 ; PME electrostatics parameters coulombtype = PME fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft= yes ; Berendsen temperature coupling is on in two groups Tcoupl = Nose-Hoover tc_grps = Protein Non-Protein tau_t = 0.5 0.5 ref_t = 310 310 ; Pressure coupling is on Pcoupl = Parrinello-Rahman pcoupltype = isotropic tau_p = 1.0 compressibility = 4.5e-5 ref_p = 1.0 refcoord_scaling = com ; Generate velocities is off gen_vel = no ; Periodic boundary conditions are on in all directions pbc = xyz ; Long-range dispersion correction DispCorr= EnerPres ; Pull code pull= umbrella pull_geometry = distance ; simple distance increase pull_dim= Y N N pull_start = yes ; define initial COM distance 0 pull_ngroups= 1 pull_group0 = CA_chA_r131 pull_group1 = CA_chB_r131 pull_rate1 = 0.01 ; 0.01 nm per ps = 10 nm per ns pull_k1 = 4200 ; kJ mol^-1 nm^-2 Thanks in advance. Nidhi On Wed, Aug 6, 2014 at 8:06 PM, Justin Lemkul jalem...@vt.edu wrote: On 8/6/14, 3:46 AM, Nidhi Katyal wrote: Hello all, I am working on protein with two chains. I would like to restrain one atom of one chain while doing steered MD. For the same reason, I have created an index file that includes that atom, then created its posre.itp file and finally included following lines at the end of topol_Protein_chainA.itp: ; Include Position restraint file #ifdef POSRES_CA_chA_r131 #include posre.itp #endif I am also pasting a small section of my topol.top file: ; Include forcefield parameters #include gromos53a6.ff/forcefield.itp ; Include chain topologies #include topol_Protein_chain_A.itp #include topol_Protein_chain_B.itp #include topol_Ion_chain_A2.itp #include topol_Ion_chain_B2.itp ; Include water topology #include gromos53a6.ff/spc.itp #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif After carrying out NPT equilibration, when I run following command: grompp -f md_pull.mdp -c npt.gro -p topol.top -n index.ndx -t npt.cpt -o pull.tpr as given in tutorial: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ gmx-tutorials/umbrella/05_pull.html I am getting following error: 215400 atoms are not part of any of the T-Coupling groups Since my pull.mdp file as the same as given in tutorial, my coupling groups are Protein and Non-Protein. I suspect there is something wrong while adding restraints using
Re: [gmx-users] can we use Area per lipid: 1.00 nm^2
On 8/7/14, 6:44 AM, neha bharti wrote: Hello All I am trying to perform MD for protein-ligand complex in popc lipid with Charmm36 force field and also follow Justin A. Lemkul tutorial. I performed perl inflategro.pl system.gro 4 POPC 0 system_inflated.pdb 5 area.dat followed by energy minimization then, perl inflategro.pl em.gro 0.95 POPC 0 system_shrink1.gro 5 area_shrink1.dat followed by energy minimization then after 16 iteration of scaling down by 0.95 I got Area per lipid: 1.00 nm^2. In 17th iteration Area per lipid become 0.80 nm^2. but after that when I visualize the .gro file i.e system_shrink17.gro the ligand molecule is far from protein and out of lipid. But till 16th iteration its inside the lipid in its normal position. Should I perform till 16th iteration which gives area per lipid 1.00 nm^2 ? Is it a good value for Area per lipid ?? Absolutely not. That's 100 A^2. InflateGRO doesn't know how to deal with ligands. You need to add the ligand in after building the protein-membrane system. -Justin or there is some error in my files. My topology file is : ; Include forcefield parameters #include charmm36_lipid.ff/forcefield.itp ; Include Position restraint file #ifdef POSRES #include posre.itp #endif This position restraint file does not correspond to any [moleculetype] and will have no effect when used (more likely you'll get a fatal error). If this is related to the protein, leave its original location alone. -Justin ; Include ligand topology #include LIG.itp ; Ligand position restraints #ifdef POSRES #include posre_LIG.itp #endif [ moleculetype ] ; Namenrexcl Protein 3 [ atoms ] . . . . . . ; Strong position restraints for InflateGRO #ifdef POSRES_STRONG #include strong_posre.itp #endif ; Include POPC chain topology #include popc.itp ; Include water topology #include charmm36_lipid.ff/tip3p.itp #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ; Include topology for ions #include charmm36_lipid.ff/ions.itp [ system ] ; Name Gyas ROwers Mature At Cryogenic Speed [ molecules ] ; Compound#mols Protein 1 LIG 1 POPC 128 Please Help Thank you very much. With Regards Neha bharty -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA 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] Velocity Distribution Calculation
Dear all, I posted it days before. But no one replied. I am wondering if someone has any suggestions about calculation of velocity distribution. Thank you very much. Best, Jason 2014-08-05 23:55 GMT-04:00 jasonzhu...@gmail.com: Dear all, I am a new user of GROMACS. Now I am using it on water permeability through a nano-channel. The pressure difference is applied by adding acceleration to water molecules in a periodic simulation box. To get the flow rate of water, I need to the number of water molecules through the channel or spatial velocity distribution in different regions. I used to do similar simulations by LAMMPS. LAMMPS provides the function of count (region, group) or the command of fix ave/spatial for counting atom number or velocity distribution. I am wondering how I can do it in GROMACS. Does it have the same commands? I went over the manual and saw commands of g_traj and g_spatial. Are they what I am looking for? Thank you very much for your attention. Best, Jason -- 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] Velocity Distribution Calculation
On 8/7/14, 7:02 AM, 朱文鹏 wrote: Dear all, I posted it days before. But no one replied. I am wondering if someone has any suggestions about calculation of velocity distribution. Select groups using g_select, extract velocities with g_traj, and create distributions with g_analyze. -Justin Thank you very much. Best, Jason 2014-08-05 23:55 GMT-04:00 jasonzhu...@gmail.com: Dear all, I am a new user of GROMACS. Now I am using it on water permeability through a nano-channel. The pressure difference is applied by adding acceleration to water molecules in a periodic simulation box. To get the flow rate of water, I need to the number of water molecules through the channel or spatial velocity distribution in different regions. I used to do similar simulations by LAMMPS. LAMMPS provides the function of count (region, group) or the command of fix ave/spatial for counting atom number or velocity distribution. I am wondering how I can do it in GROMACS. Does it have the same commands? I went over the manual and saw commands of g_traj and g_spatial. Are they what I am looking for? Thank you very much for your attention. Best, Jason -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA 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] Restrain the COM of a reference group in Umbrella sampling
Hi All, I'm calculating the PMF of pulling a surfactant molecule from a polymer slab in aqueous phase. Therefore, my pull group is the surfactant and the reference group is the slab. To prevent the reference group (slab) from being dragged by the pull group (surfactant), I would like to restrain the COM of my reference group, instead of restraining all atoms in the reference group. I did this by removing the COM motion of my reference group using comm_grps mdp options. In addition, I also removed the COM motion of other atoms, including waters and ions in the system so that there are no external forces applying to the system. Therefore, I have two comm_grps: slab Waters and ion. As you may notice, my comm_grps does not include the pull group (surfactant), which triggers a warning by grompp, saying Some atoms are not part of any center of mass motion removal group. This may lead to artifacts. I could have included the surfactant in the group of waters and ions but the fact that this surfactant is moving by an umbrella potential refrains me from doing so. My question is: 1. Does this seem to be a reasonable choice to restrain the COM of a reference group? 2. I have two groups in the removal of COM motion. Does this suggest I should also use the same two groups for temperature coupling? 3. For a MD step using a leapfrog algorithm, when does the COM removal happen? Does it occur after applying corrections due to constraints and before re-scaling the coordinates and box due to pressure coupling? cheers, -- 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] Gromacs 5.0 installation
Hello. Just take the .tar.gz on a thumb drive to your new machine and install from that. Note that this machine will already need to have all the prerequisites. If not, you will need to install those first: cmake gcc Don’t forget fftw lapack and blas. You can use the ones built in gromacs with appropriate cmake flags but they are slow. Dan GMU On Aug 7, 2014, at 2:01 AM, Fatemeh Dabbagh daba...@sums.ac.ir wrote: Hi everyone, I'm trying to install Gromacs 5.0 on a computer which has no network connection. It would be appreciated if some one tell me how this can be done! Regards Fatemeh -- 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] how to write in a script?
Try this: echo -e 1|14\nq\r | make_ndx -f input.pdb Hope it works! o/ 2014-08-07 9:52 GMT-03:00 Albert mailmd2...@gmail.com: Hi Joao: thanks a lot for kind reply. I don't get the point how to use it properly. I am trying to insert #ifdef POSRES_UNK betwee the following two lines: ; position restraints for System of [ position_restraints ] It should be looks like the following after script: ; position restraints for System of #ifdef POSRES_UNK [ position_restraints ] can you elaberate more how to use it? I tried to run it with command: cat tmp.itp ligand.itp EOF ? #ifdef POSRES_UNK ? EOF it seems doesn't work... THX Albert On 08/07/2014 02:37 PM, João Henriques wrote: Something like this. Edit it according to your needs. cat file EOF #ifdef POSRES_UNK EOF -- 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. -- M.Sc. Maurício Menegatti Rigo Núcleo de Bioinformática do Laboratório de Imunogenética Departamento de Genética Instituto de Biociências Universidade Federal do Rio Grande do Sul - Campus do Vale Av. Bento Gonçalves, 9500 - Bairro Agronomia - Prédio 43323 M CEP:91501-970 Caixa Postal 15053 Porto Alegre, RS, Brasil Tel: +55 51 3308 9938 -- 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] New residue in FF does not bond to others.
http://www.speedyshare.com/9EhEf/charm27-files.tar.bz2 http://www.speedyshare.com/AMWM7/mCherry7.tar.bz2 Like I said they are the same except two extra lines in aminoacids.rtp file. 2014-08-07 2:27 GMT+01:00 Justin Lemkul jalem...@vt.edu: On 8/6/14, 1:36 PM, Dawid das wrote: These are lines that cause trouble: ERROR 1 [file mCherry7.top, line 18183]: No default U-B types ERROR 2 [file mCherry7.top, line 18250]: No default U-B types ERROR 3 [file mCherry7.top, line 25379]: No default Proper Dih. types ERROR 4 [file mCherry7.top, line 25380]: No default Proper Dih. types ERROR 5 [file mCherry7.top, line 25383]: No default Proper Dih. types ERROR 6 [file mCherry7.top, line 25386]: No default Proper Dih. types ERROR 7 [file mCherry7.top, line 25387]: No default Proper Dih. types ERROR 8 [file mCherry7.top, line 25388]: No default Proper Dih. types ERROR 9 [file mCherry7.top, line 25455]: No default Proper Dih. types ERROR 10 [file mCherry7.top, line 25457]: No default Proper Dih. types ERROR 11 [file mCherry7.top, line 25458]: No default Proper Dih. types Now in these files which I have already uploaded I have only added two extra lines just above [ angles ] section of CH6 residue in aminoacids.rtp (lines 1793 and 1794): MC3 +N 0.1345 154808.0 MN1 -C 0.139 173594.2 I have not changed anything else in any other file. Now the problem is that I have consecutive residues Phe65-CH6-Ser69. MN1 atom of CH6 is supposed to be bonded to C atom of Phe65. MC3 atom of CH6 is supposed to be bonded to atom NH1 of Ser69. C atom of Phe65 is not supposed to be bonded to NH1 atom of Ser69 but it is in my *top file. What other files do you need? The same ones you provided before. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA 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. -- 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] Eigenvalues not saved from gmx covar in GROMACS 5
I have installed v5 of GROMACS and am doing simulations on a peptide VPGVG repeated five times. I am trying to calculate entropy and the eigenvalues of the covariance matrix to get eigenfrequencies. When I issue the command gmx covar -f full.trr -s full.tpr -v -o -mwa (for eigenvalues), I get an empty eigenvalues.xvg. In GROMACS v4.5.5 I used to get the eigenvalues outputted, for the same data sets, same command (g_covar). It says it's writing the eigenvalues, but when I open the file there are no eigenvalues there, only the preamble for the xvg file, ending at @TYPE xy. What am I doing wrong or is this a bug? Thank you, -Steven -- 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.
