Re: [gmx-users] Re: extreme projections
Hi, If you have VMD installed, load the extreme.pdb. Then in graphics Representations---Trajectory--- put values in Draw Multiple Frames, for e.g. 0:10 this will show the extremes of 0th frame to 10th frame (you can change this a/c to your representation). After this selecting Draw style--- coloring method--- trajectory--- time step: this will help you to show the deviation in frames via different coloring. On Mon, Jul 15, 2013 at 5:12 AM, Ahmet yıldırım ahmedo...@gmail.com wrote: any one please help me out with this problem? 2013/7/10 Ahmet yıldırım ahmedo...@gmail.com Dear users, I extracted separate extreme projections using g_anaeig. I have to make pictures which show the difference. Can you help me, someone who makesthem using pymolbefore ? -- Ahmet Yıldırım -- Ahmet Yıldırım -- 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 -- With Regards, Rashmi Kumari Research Scholar School of Computational and Integrative Sciences Jawaharlal Nehru University New Delhi- 110067. -- 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] Chlorate ion force field
I am afraid you will need to derive it from scratch. There should be some studies about perchlorate salts in literature. Make a search. Dr. Vitaly V. Chaban On Tue, Jul 16, 2013 at 6:08 AM, Sushma Yadav sushc...@gmail.com wrote: Dear users, How do I get the force-field for ClO4- ion in the gromacs? Thanks in advance. -- 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 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] entropy calculation
Hi gmx users I took a natural protein fold and unfolded with simulated annealing molecular dynamics (SAMD). Now I have folded and unfolded structure. I want to calculate statistically entropy difference of the two system. Can we do with gromacs??? what is the correct protocol ?? best pooja -- 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] aminoacids protonation in different ph
Dear Justin I found a server : http://biophysics.cs.vt.edu/ that protonate aminoacids according to desired pH easily. Sincerely Fatemeh Ramezani -- 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] make an index file of COM of lipid bilayer
Hi, Would you please let me know how can I make an index file of COM of lipid membrane? I guess the position of the COM of the bilayer, but how it is possible to make an index file of this point? I want to include this index file as the ref_group in Umbrella Sampling. Sincerely, Shima -- 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] Chlorate ion force field
Hello, I hope the following paper may help you http://pubs.acs.org/doi/pdf/10.1021/j100286a020 regards Srinivas On Tue, Jul 16, 2013 at 9:54 AM, Dr. Vitaly Chaban vvcha...@gmail.comwrote: I am afraid you will need to derive it from scratch. There should be some studies about perchlorate salts in literature. Make a search. Dr. Vitaly V. Chaban On Tue, Jul 16, 2013 at 6:08 AM, Sushma Yadav sushc...@gmail.com wrote: Dear users, How do I get the force-field for ClO4- ion in the gromacs? Thanks in advance. -- 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 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 -- Ability is what gives you the opportunity and belief is what gets you there, but it's important to have the right attitude as that determines your success or failure ** Srinivasa Rao Varanasi Guest Researcher Theory of Polymers group Leibniz Institute for Polymer Research Hohe Straße 6, Dresden, 01069. Germany. -- 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] application of MM-GBSA
Hello sir, I require to calculate binding energy using MM-GBSA method. I searched through the manual but i did not find any. i request you to kindly guide to as to which manual to follow to identify binding energy. Thanking You with Regards. Arunima Shilpi Ph. D Research Scholar(Cancer Epigenetics) Department of Life Science National Institute of Technology Rourkela Odisha -- 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] Reverse_MICELLEFatel error, moleculetype SOL is redefined
On 7/16/13 1:02 AM, Hari Pandey wrote: Hi Gromaxers, Thanks for previous answers. I have to simulate reverse micelle after solvation with isooctane.My system now is: ISOOCTANE(solvent)+AOT(surfactant)+coreWATER. When I do grompp, it says moleculetype SOL is redefined and lots of another errors. Please advice me how do I do reverse micelle simulation. What I did is:: (1) pdb2gmx -f RM.pdb -o RM.gro -p RM.top step I choose isooctane as water model. I have isooctane.itp in the file watermodel.dat inside my forcefield. (2) editconf -c -f RM.gro -o RM1.gro -p RM.top -bt dodecahedron -d 2.0 -shell 0.3 (3) genbox -cp RM.gro -cs isooctane.gro -p reverse_RM.top -o RM2.pdb (4) grompp -f em.mdp -c RM2.pdb -p RM.top -n index.ndx -o em.tpr -maxwarn 5 where RM.pdb is pdb file of reverse micelle All required files I have ,and I have index.ndx file also But it returns : Fatel error: the moleculetype SOL is redefined I tried lots, I change the SOL to WATER every where in frocefield as well as my .gro file too. I tried all what I could but no get any benifit. So You have two topologies that define a [moleculetype] named SOL, which causes the error. Likely it's somewhere in the isooctane.itp file, because you seem to be treating it like water above (which is unnecessary). -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 == -- 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] entropy calculation
On 7/16/13 4:30 AM, pooja_gu...@nccs.res.in wrote: Hi gmx users I took a natural protein fold and unfolded with simulated annealing molecular dynamics (SAMD). Now I have folded and unfolded structure. I want to calculate statistically entropy difference of the two system. Can we do with gromacs??? what is the correct protocol ?? g_anaeig allows for the calculation of entropy based on the quasiharmonic approach. -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 == -- 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] make an index file of COM of lipid bilayer
On 7/16/13 5:30 AM, Shima Arasteh wrote: Hi, Would you please let me know how can I make an index file of COM of lipid membrane? I guess the position of the COM of the bilayer, but how it is possible to make an index file of this point? I want to include this index file as the ref_group in Umbrella Sampling. Index files can't specify positions, only atoms. In this case, you don't even need a special index group - just use the membrane. The pull code uses the COM of the selected group, so if you specify your membrane, mdrun knows to use its COM. -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 == -- 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
Fw: [gmx-users] make an index file of COM of lipid bilayer
Thanks for your reply. But would you please tell me what is known for the pull_group line? I mean are the atom names or resid-s or residue names or know for it? Sincerely, Shima - Forwarded Message - From: Justin Lemkul jalem...@vt.edu To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Tuesday, July 16, 2013 3:39 PM Subject: Re: [gmx-users] make an index file of COM of lipid bilayer On 7/16/13 5:30 AM, Shima Arasteh wrote: Hi, Would you please let me know how can I make an index file of COM of lipid membrane? I guess the position of the COM of the bilayer, but how it is possible to make an index file of this point? I want to include this index file as the ref_group in Umbrella Sampling. Index files can't specify positions, only atoms. In this case, you don't even need a special index group - just use the membrane. The pull code uses the COM of the selected group, so if you specify your membrane, mdrun knows to use its COM. -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 == -- 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: Fw: [gmx-users] make an index file of COM of lipid bilayer
On 7/16/13 7:41 AM, Shima Arasteh wrote: Thanks for your reply. But would you please tell me what is known for the pull_group line? I mean are the atom names or resid-s or residue names or know for it? Like everything in Gromacs, these are just group names. You can use either default groups (http://www.gromacs.org/Documentation/Terminology/Default_Index_Groups) or groups of your own creation. The names specified must match either a default group name or a group name found in an index file. See my umbrella sampling tutorial for examples. -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 == -- 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] Problem with energy minimization parameters
On 7/16/13 11:05 AM, Sainitin Donakonda wrote: Hi all, I have 3 protein-drug complexes (same protein and different drugs) i performed 20 ns molecular dynamics simulation..using same parameters (i mean energy minimzation parameters) ..2 of them was successful for MD simulation..(im using Charmm 27 Force field) But 1 drug protein complex is failed in Energy minimization step itself.. showing following error *Error : whole protein drug complex * * * *708 particles communicated to PME node 2 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension x.* *This usually means that your system is not well equilibrated * Then i looked up http://www.gromacs.org/Documentation/Terminology/Blowing_Up In this i followed up suggestions which are mentioned in diagnosing unstable system as follows. First i did energy minimization for protein alone which worked perfectly with out any error. Second i did energy minimization for ligand alone (with out protein)..this showed again following error.. Error 2 : Ligand only Fatal error: *184 particles communicated to PME node 2 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension x. This usually means that your system is not well equilibrated.* So there is problem with small molecule...not with the protein ..here i think i should tune parameters in .MDP file..which i m just not getting how to do.. here is the EM.mdp file.. ; LINES STARTING WITH ';' ARE COMMENTS title= Minimization; Title of run define = -DFLEX_TI3P; defines to pass to the preprocessor constraints = none ; 7.3.3 Run Control integrator = steep ; steepest descents energy minimization nsteps = 2000 ; maximum number of steps to integrate energygrps = LIG; group(s) to write to energy file ; 7.3.5 Energy Minimization emtol = 1000 ; [kJ/mol/nm] minimization is converged when max force is emtol emstep = 0.01 ; [nm] initial step-size dt = 0.01 ; 7.3.9 Neighbor Searching nstlist = 1; [steps] freq to update neighbor list nstxout = 1 ns_type = grid ; method of updating neighbor list pbc = xyz ; periodic boundary conditions in all directions rlist = 1.2 ; [nm] cut-off distance for the short-range neighbor list rlistlong = 1.4 ; [nm] Cut-off distance from the long-range neighbor list ; 7.3.10 Electrostatics coulombtype = PME ; Particle-Mesh Ewald electrostatics rcoulomb= 1.2 ; [nm] distance for Coulomb cut-off ; 7.3.11 VdW vdwtype = switch ; twin-range cut-off with rlist where rvdw = rlist rvdw= 1.2 ; [nm] distance for LJ cut-off rvdw_switch = 0.2 ; Start switching th LJ potential DispCorr= Ener ; apply long range dispersion corrections for energy ; 7.3.13 Ewald fourierspacing = 0.12 ; [nm] grid spacing for FFT grid when using PME fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ; interpolation order for PME, 4 = cubic ewald_rtol = 1e-5 ; relative strength of Ewald-shifted potential at rcoulomb optimize_fft= yes Can any body please tell me how to optimize these parameters The value of rvdw_switch should be 1.0 for correct usage of the force field. One should not seek to optimize the .mdp settings when something is crashing. Fixing errors (like rvdw_switch here) is one thing, but beyond that you shouldn't do any adjusting. More often than not, in a case like yours where a molecule in vacuo blows up, the topology is the problem. -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 == -- 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] Problem with energy minimization parameters
Hi all, I have 3 protein-drug complexes (same protein and different drugs) i performed 20 ns molecular dynamics simulation..using same parameters (i mean energy minimzation parameters) ..2 of them was successful for MD simulation..(im using Charmm 27 Force field) But 1 drug protein complex is failed in Energy minimization step itself.. showing following error *Error : whole protein drug complex * * * *708 particles communicated to PME node 2 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension x.* *This usually means that your system is not well equilibrated * Then i looked up http://www.gromacs.org/Documentation/Terminology/Blowing_Up In this i followed up suggestions which are mentioned in diagnosing unstable system as follows. First i did energy minimization for protein alone which worked perfectly with out any error. Second i did energy minimization for ligand alone (with out protein)..this showed again following error.. Error 2 : Ligand only Fatal error: *184 particles communicated to PME node 2 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension x. This usually means that your system is not well equilibrated.* So there is problem with small molecule...not with the protein ..here i think i should tune parameters in .MDP file..which i m just not getting how to do.. here is the EM.mdp file.. ; LINES STARTING WITH ';' ARE COMMENTS title= Minimization; Title of run define = -DFLEX_TI3P; defines to pass to the preprocessor constraints = none ; 7.3.3 Run Control integrator = steep ; steepest descents energy minimization nsteps = 2000 ; maximum number of steps to integrate energygrps = LIG; group(s) to write to energy file ; 7.3.5 Energy Minimization emtol = 1000 ; [kJ/mol/nm] minimization is converged when max force is emtol emstep = 0.01 ; [nm] initial step-size dt = 0.01 ; 7.3.9 Neighbor Searching nstlist = 1; [steps] freq to update neighbor list nstxout = 1 ns_type = grid ; method of updating neighbor list pbc = xyz ; periodic boundary conditions in all directions rlist = 1.2 ; [nm] cut-off distance for the short-range neighbor list rlistlong = 1.4 ; [nm] Cut-off distance from the long-range neighbor list ; 7.3.10 Electrostatics coulombtype = PME ; Particle-Mesh Ewald electrostatics rcoulomb= 1.2 ; [nm] distance for Coulomb cut-off ; 7.3.11 VdW vdwtype = switch ; twin-range cut-off with rlist where rvdw = rlist rvdw= 1.2 ; [nm] distance for LJ cut-off rvdw_switch = 0.2 ; Start switching th LJ potential DispCorr= Ener ; apply long range dispersion corrections for energy ; 7.3.13 Ewald fourierspacing = 0.12 ; [nm] grid spacing for FFT grid when using PME fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ; interpolation order for PME, 4 = cubic ewald_rtol = 1e-5 ; relative strength of Ewald-shifted potential at rcoulomb optimize_fft= yes Can any body please tell me how to optimize these parameters Thanks, Nitin -- 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] Exclude ions from spherical region
I am in the process of evaluating whether Gromacs is suitable for a simulation that I'm planning to conduct, and I was hoping that more experienced users might provide insight into whether the following is possible: I want to exclude a subset of molecules (i.e. all but one or two ions in the system) from a spherical region centered at the origin using a half-harmonic restraint. In this setup, the ions would not feel an external force if they were a distance greater than R away from (0, 0, 0), and but they would be repelled from the excluded sphere with some appropriate force constant at distance less than R. I looked at the distance restraint feature, which appears to have the capability of providing a restraint with a half-harmonic shape. I believe if I set r_1 from Fig 4.13 in the 4.6.3 Manual (up1) to a distance larger than the simulation box's extent this would get me a restraint of the correct function form (unless I'm missing a subtly of how it works). However, it looks like this must be defined between two explicit atoms, whereas I want the distance measured between an atom and a point in the lab frame. I also looked at the pull code, which appears to provide a way of measuring distances from the origin by leaving pull-group0 empty. This functionality, however, does not appear to support a flat bottom region in the restraint. Unless I'm mistaken, it looks like the only option is to have a standard harmonic restraint via the umbrella option. If anyone has insight into how to get the desired functionality using Gromacs. I would appreciate it. I have seen some suggestion on the list for a hacked in version of a flat-bottom potential, but I would prefer a solution that didn't involve modifying the code if possible. Best wishes, Josh -- 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: Problem with energy minimization parameters
Hi Justin, Thanks for suggestion...and pointing out that there is problem with topology ...now i checked ligand file..there hydrogens were not added correctly..so swissparam tool was not correct topology .. now i corrected it ..it works perfectly .. Thanks a lot Sainitin On Tue, Jul 16, 2013 at 5:05 PM, Sainitin Donakonda saigr...@gmail.comwrote: Hi all, I have 3 protein-drug complexes (same protein and different drugs) i performed 20 ns molecular dynamics simulation..using same parameters (i mean energy minimzation parameters) ..2 of them was successful for MD simulation..(im using Charmm 27 Force field) But 1 drug protein complex is failed in Energy minimization step itself.. showing following error *Error : whole protein drug complex * * * *708 particles communicated to PME node 2 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension x.* *This usually means that your system is not well equilibrated * Then i looked up http://www.gromacs.org/Documentation/Terminology/Blowing_Up In this i followed up suggestions which are mentioned in diagnosing unstable system as follows. First i did energy minimization for protein alone which worked perfectly with out any error. Second i did energy minimization for ligand alone (with out protein)..this showed again following error.. Error 2 : Ligand only Fatal error: *184 particles communicated to PME node 2 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension x. This usually means that your system is not well equilibrated.* So there is problem with small molecule...not with the protein ..here i think i should tune parameters in .MDP file..which i m just not getting how to do.. here is the EM.mdp file.. ; LINES STARTING WITH ';' ARE COMMENTS title= Minimization; Title of run define = -DFLEX_TI3P; defines to pass to the preprocessor constraints = none ; 7.3.3 Run Control integrator = steep ; steepest descents energy minimization nsteps = 2000 ; maximum number of steps to integrate energygrps = LIG; group(s) to write to energy file ; 7.3.5 Energy Minimization emtol = 1000 ; [kJ/mol/nm] minimization is converged when max force is emtol emstep = 0.01 ; [nm] initial step-size dt = 0.01 ; 7.3.9 Neighbor Searching nstlist = 1; [steps] freq to update neighbor list nstxout = 1 ns_type = grid ; method of updating neighbor list pbc = xyz ; periodic boundary conditions in all directions rlist = 1.2 ; [nm] cut-off distance for the short-range neighbor list rlistlong = 1.4 ; [nm] Cut-off distance from the long-range neighbor list ; 7.3.10 Electrostatics coulombtype = PME ; Particle-Mesh Ewald electrostatics rcoulomb= 1.2 ; [nm] distance for Coulomb cut-off ; 7.3.11 VdW vdwtype = switch ; twin-range cut-off with rlist where rvdw = rlist rvdw= 1.2 ; [nm] distance for LJ cut-off rvdw_switch = 0.2 ; Start switching th LJ potential DispCorr= Ener ; apply long range dispersion corrections for energy ; 7.3.13 Ewald fourierspacing = 0.12 ; [nm] grid spacing for FFT grid when using PME fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ; interpolation order for PME, 4 = cubic ewald_rtol = 1e-5 ; relative strength of Ewald-shifted potential at rcoulomb optimize_fft= yes Can any body please tell me how to optimize these parameters Thanks, Nitin -- 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 4.6.1, Expanded ensemble: weird balancing factors
I have a similar question here. Can anyone tell if the Wang-Landau algorithm in lambda space is robust in that it doesn't depend on the choice of the convergence factor (weight-equil-wl-delta), the flatness of the histogram (wl-ratio) and/or the frequency of trial move (nstexpanded), especially in the case of barely overlapping energy distribution corresponding to different lambdas? I can imagine in the extreme case, with only 2 lambdas ( l = 1 or 0), the gap between the 2 energy distributions might be so large such that for most of the time, trial moves from the center of distribution 1 would frequently end up in the tail of distribution 0. In this case, the Wang-Landau weights would be biased if there's not enough time for the system to relax back to equilibrium. Thanks, Dejun -- View this message in context: http://gromacs.5086.x6.nabble.com/gmx-4-6-1-Expanded-ensemble-weird-balancing-factors-tp5007681p5009892.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] Bilayer curvature
Dear All, I have set two bilayers: 1. 400 DOPC 2. 320DOPC and 80 Cardiolipin Second one show significant curvature during NPT equilibrium and MD run (not in NVT eq.). Is it normal? For the first bilayer, after adding the protein to the system, here also I can see big curvature in the membrane. Does anybody knows is it normal or something is wrong? Which factors do affect the membrane curvature (like: initial conf., water, ions, box size, equilibration steps, ...)? Thanks, Dariush -- 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] window exchange umbrella sampling
I am trying to use Hamiltonian replica exchange as implemented in Gromacs. The idea is to use different pulling umbrella forces and then obtain a PMF profile. I am specifically interested in exchanging force constants between windows. To do a quick test, I successfully ran replica exchange in which the temperature is exchanged. In this case, I prepared for example 8 tpr files at 8 different temperatures and run them using mpirun -np 8 mdrun_mpi -s prefix_.tpr -multi 8 -replex 100 And it ran just fine. For window exchange umbrella sampling, though, I am confused with the input preparation. I am not sure how to specify in the .mdp file how the values of pull force should be used to define different force constants for different replicas. Also, when submitting the job, how should I ask the program to exchange pull forces between windows? I tried using this: http://lists.gromacs.org/pipermail/gmx-users/2011-April/060448.html But, it gives me the error: Fatal error: The properties of the ... systems are all the same, there is nothing to exchange I noticed a previous discussion on below link: http://gromacs.5086.x6.nabble.com/Hamiltonian-replica-exchange-umbrella-sampling-with-gmx-4-6-td5006187.html However, I am not sure how to use the restraint-lambda parameter exactly. Is there any example, ... how to use it? I have copied the related portion of one of the the .mdp files below for moving MOL2 with respect to MOL1 Thanks for your help, Parisa . . . pull_group0 = MOL1 pull_weights0= pull_pbcatom0= 0 pull_group1 = MOL2 pull_weights1= pull_pbcatom1= 0 pull_vec1= 0.0 0.0 0.0 pull_init1 = 0.0 0.0 0.0 pull_rate1 = 0 pull_k1 = 300 free_energy = yes restraint-lambdas = 0.0 0.5 1.0 0.0 0.5 1.0 0.0 0.5 1.0 . . . -- 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] Re: gmx 4.6.1, Expanded ensemble: weird balancing factors
Hi, all- This not a problem with W-L, but is instead something that is wrong with a particular combination of mdp options that are not working for expanded ensemble simulations. W-L can equilibrate to incorrect distributions because it decreases the weights too fast (more on that later), but that is not the problem here. The option wl-oneovert allows switching to a slower scaling that is more likely to converge. The reason that it is not a W-L problem is that after the WL weights are equilibrated, it is equilibrium sampling in the expanded ensemble. If the W-L equilibration was a problem, then the distribution of states would not be flat. They are flat, so therefore the expanded ensemble dynamics are wrong. I have example expanded ensemble setups. http://www.alchemistry.org/wiki/GROMACS_4.6_example:_Ethanol_solvation_with_expanded_ensemble These mdp files should work. Note that you should be able to swap out any top, and it will still work. If you get CORRECT results (and it should take just a few ns to see) with these tops, then I will go through and try to figure out which differences are causing the problems. Thanks for the patience while we test this new functionality. Frequently when one puts new code in the hands of others it breaks in ways that were not foreseen! On Tue, Jul 16, 2013 at 12:53 PM, Dejun Lin dejun@gmail.com wrote: I have a similar question here. Can anyone tell if the Wang-Landau algorithm in lambda space is robust in that it doesn't depend on the choice of the convergence factor (weight-equil-wl-delta), the flatness of the histogram (wl-ratio) and/or the frequency of trial move (nstexpanded), especially in the case of barely overlapping energy distribution corresponding to different lambdas? I can imagine in the extreme case, with only 2 lambdas ( l = 1 or 0), the gap between the 2 energy distributions might be so large such that for most of the time, trial moves from the center of distribution 1 would frequently end up in the tail of distribution 0. In this case, the Wang-Landau weights would be biased if there's not enough time for the system to relax back to equilibrium. Thanks, Dejun -- View this message in context: http://gromacs.5086.x6.nabble.com/gmx-4-6-1-Expanded-ensemble-weird-balancing-factors-tp5007681p5009892.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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 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] window exchange umbrella sampling
You need to have different pull parameters at the end states. Right now, pull-kB1 is not defined in your code, so there is nothing to interpolate to: it assume pull-kB1 = pull-k1. Longer scale -- one would want to define reference distances that change with lambda within the same simulation, but looking over the code, I'm not seeing anything. One would want to add a pull_vect1B to change the location of the restraint as a function of lambda, but this isn't yet defined. That should be something we look at in the future . . . On Tue, Jul 16, 2013 at 2:41 PM, Parisa Akhshi akhshi...@gmail.com wrote: I am trying to use Hamiltonian replica exchange as implemented in Gromacs. The idea is to use different pulling umbrella forces and then obtain a PMF profile. I am specifically interested in exchanging force constants between windows. To do a quick test, I successfully ran replica exchange in which the temperature is exchanged. In this case, I prepared for example 8 tpr files at 8 different temperatures and run them using mpirun -np 8 mdrun_mpi -s prefix_.tpr -multi 8 -replex 100 And it ran just fine. For window exchange umbrella sampling, though, I am confused with the input preparation. I am not sure how to specify in the .mdp file how the values of pull force should be used to define different force constants for different replicas. Also, when submitting the job, how should I ask the program to exchange pull forces between windows? I tried using this: http://lists.gromacs.org/pipermail/gmx-users/2011-April/060448.html But, it gives me the error: Fatal error: The properties of the ... systems are all the same, there is nothing to exchange I noticed a previous discussion on below link: http://gromacs.5086.x6.nabble.com/Hamiltonian-replica-exchange-umbrella-sampling-with-gmx-4-6-td5006187.html However, I am not sure how to use the restraint-lambda parameter exactly. Is there any example, ... how to use it? I have copied the related portion of one of the the .mdp files below for moving MOL2 with respect to MOL1 Thanks for your help, Parisa . . . pull_group0 = MOL1 pull_weights0= pull_pbcatom0= 0 pull_group1 = MOL2 pull_weights1= pull_pbcatom1= 0 pull_vec1= 0.0 0.0 0.0 pull_init1 = 0.0 0.0 0.0 pull_rate1 = 0 pull_k1 = 300 free_energy = yes restraint-lambdas = 0.0 0.5 1.0 0.0 0.5 1.0 0.0 0.5 1.0 . . . -- 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 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] Re: gmx 4.6.1, Expanded ensemble: weird balancing factors
Hi Michael, Thanks for the reply. Just a quick follow-up. Do you think the overlap of energy histogram between different lambdas matter for lambda-dynamics in general? (Maybe not in this particular case or in the case of the tutorial you just posted.) I wonder if we need as many intermediate lambdas as in the case of replica exchange since the weights compensate the difference in energy. Thanks, Dejun 2013/7/16 Michael Shirts mrshi...@gmail.com Hi, all- This not a problem with W-L, but is instead something that is wrong with a particular combination of mdp options that are not working for expanded ensemble simulations. W-L can equilibrate to incorrect distributions because it decreases the weights too fast (more on that later), but that is not the problem here. The option wl-oneovert allows switching to a slower scaling that is more likely to converge. The reason that it is not a W-L problem is that after the WL weights are equilibrated, it is equilibrium sampling in the expanded ensemble. If the W-L equilibration was a problem, then the distribution of states would not be flat. They are flat, so therefore the expanded ensemble dynamics are wrong. I have example expanded ensemble setups. http://www.alchemistry.org/wiki/GROMACS_4.6_example:_Ethanol_solvation_with_expanded_ensemble These mdp files should work. Note that you should be able to swap out any top, and it will still work. If you get CORRECT results (and it should take just a few ns to see) with these tops, then I will go through and try to figure out which differences are causing the problems. Thanks for the patience while we test this new functionality. Frequently when one puts new code in the hands of others it breaks in ways that were not foreseen! On Tue, Jul 16, 2013 at 12:53 PM, Dejun Lin dejun@gmail.com wrote: I have a similar question here. Can anyone tell if the Wang-Landau algorithm in lambda space is robust in that it doesn't depend on the choice of the convergence factor (weight-equil-wl-delta), the flatness of the histogram (wl-ratio) and/or the frequency of trial move (nstexpanded), especially in the case of barely overlapping energy distribution corresponding to different lambdas? I can imagine in the extreme case, with only 2 lambdas ( l = 1 or 0), the gap between the 2 energy distributions might be so large such that for most of the time, trial moves from the center of distribution 1 would frequently end up in the tail of distribution 0. In this case, the Wang-Landau weights would be biased if there's not enough time for the system to relax back to equilibrium. Thanks, Dejun -- View this message in context: http://gromacs.5086.x6.nabble.com/gmx-4-6-1-Expanded-ensemble-weird-balancing-factors-tp5007681p5009892.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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 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 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] Re: gmx 4.6.1, Expanded ensemble: weird balancing factors
That's a good question. My understanding and experience is the difference in required overlap in replica exchange and expanded ensemble methods is not significant. There are probably some more detailed studies out there. Expanded ensemble can be somewhat more efficient (see a paper by Park and Pande) But you really do want to have at least 30% of the states moving each time in any case. However, you DO need less overlap to get fairly good free energy estimates. I.e. the overlap for BAR to work fairly well is lower than the what you need for good mixing. That's more anecdotal -- I'd have to dig a bit to get you good results on that . . . On Tue, Jul 16, 2013 at 3:19 PM, Dejun Lin dejun@gmail.com wrote: Hi Michael, Thanks for the reply. Just a quick follow-up. Do you think the overlap of energy histogram between different lambdas matter for lambda-dynamics in general? (Maybe not in this particular case or in the case of the tutorial you just posted.) I wonder if we need as many intermediate lambdas as in the case of replica exchange since the weights compensate the difference in energy. Thanks, Dejun 2013/7/16 Michael Shirts mrshi...@gmail.com Hi, all- This not a problem with W-L, but is instead something that is wrong with a particular combination of mdp options that are not working for expanded ensemble simulations. W-L can equilibrate to incorrect distributions because it decreases the weights too fast (more on that later), but that is not the problem here. The option wl-oneovert allows switching to a slower scaling that is more likely to converge. The reason that it is not a W-L problem is that after the WL weights are equilibrated, it is equilibrium sampling in the expanded ensemble. If the W-L equilibration was a problem, then the distribution of states would not be flat. They are flat, so therefore the expanded ensemble dynamics are wrong. I have example expanded ensemble setups. http://www.alchemistry.org/wiki/GROMACS_4.6_example:_Ethanol_solvation_with_expanded_ensemble These mdp files should work. Note that you should be able to swap out any top, and it will still work. If you get CORRECT results (and it should take just a few ns to see) with these tops, then I will go through and try to figure out which differences are causing the problems. Thanks for the patience while we test this new functionality. Frequently when one puts new code in the hands of others it breaks in ways that were not foreseen! On Tue, Jul 16, 2013 at 12:53 PM, Dejun Lin dejun@gmail.com wrote: I have a similar question here. Can anyone tell if the Wang-Landau algorithm in lambda space is robust in that it doesn't depend on the choice of the convergence factor (weight-equil-wl-delta), the flatness of the histogram (wl-ratio) and/or the frequency of trial move (nstexpanded), especially in the case of barely overlapping energy distribution corresponding to different lambdas? I can imagine in the extreme case, with only 2 lambdas ( l = 1 or 0), the gap between the 2 energy distributions might be so large such that for most of the time, trial moves from the center of distribution 1 would frequently end up in the tail of distribution 0. In this case, the Wang-Landau weights would be biased if there's not enough time for the system to relax back to equilibrium. Thanks, Dejun -- View this message in context: http://gromacs.5086.x6.nabble.com/gmx-4-6-1-Expanded-ensemble-weird-balancing-factors-tp5007681p5009892.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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 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 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 mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at
[gmx-users] Re: window exchange umbrella sampling
Thanks for quick reply. I fixed the issue with kB1. Below is what I have changed in the .mdp file. I use this to run it mpirun -np 3 mdrun_mpi -s prefix_.tpr -multi 3 -replex 6 -dhdl a.dhdl. But I get this error (I am using version 4.6.1): Fatal error: Function type U-B not implemented in ip_pert For more information and tips for troubleshooting, please check the GROMACS Here is the input file: . . . pull_group0 = POPC pull_weights0= pull_pbcatom0= 0 pull_group1 = DNA pull_weights1= pull_pbcatom1= 0 pull_vec1= 0.0 0.0 0.0 pull_init1 = 0.0 0.0 0.0 pull_rate1 = 0 pull_k1 = 300 pull_kB1 = 200 free_energy = yes restraint-lambdas = 1.0 0.5 0.0 init-lambda-state = 0 nstdhdl = 10 . . . Any idea about it? Thanks, Parisa -- View this message in context: http://gromacs.5086.x6.nabble.com/window-exchange-umbrella-sampling-tp5009894p5009899.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] Bilayer curvature
On 7/16/13 3:43 PM, Dariush Mohammadyani wrote: Dear All, I have set two bilayers: 1. 400 DOPC 2. 320DOPC and 80 Cardiolipin Second one show significant curvature during NPT equilibrium and MD run (not in NVT eq.). Is it normal? You could be undergoing some sort of phase transition, but in the absence of a lot more information, it's hard to say. Pronounced curvature of a small patch of lipids sounds odd. For the first bilayer, after adding the protein to the system, here also I can see big curvature in the membrane. Some proteins induce membrane curvature, but I suspect if you were working with one of those, you'd know that curvature is normal in those cases :) Hydrophobic mismatch can play a role in perturbing lipid dynamics. Does anybody knows is it normal or something is wrong? Which factors do affect the membrane curvature (like: initial conf., water, ions, box size, equilibration steps, ...)? Force field, temperature, .mdp settings, you name it - membranes can be very finicky. It would help to have: 1. Links to where you have posted illustrative images 2. What force field you're using and your .mdp 3. What protein you're working with (if you can say) -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 == -- 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] Re: window exchange umbrella sampling
Ah, this is a force field issue -- urey-bradley terms are not supported free energy calculations. However, since only restraints are changing, this warning doesn't really need to be there. It would be relatively simple to put in a check to allow this to work, but it might take a week or two to get around to it. I'll file a redmine in the meantime, in case someone else can get to it first! http://redmine.gromacs.org/issues/1302 On Tue, Jul 16, 2013 at 5:32 PM, Parisa akhshi...@gmail.com wrote: Thanks for quick reply. I fixed the issue with kB1. Below is what I have changed in the .mdp file. I use this to run it mpirun -np 3 mdrun_mpi -s prefix_.tpr -multi 3 -replex 6 -dhdl a.dhdl. But I get this error (I am using version 4.6.1): Fatal error: Function type U-B not implemented in ip_pert For more information and tips for troubleshooting, please check the GROMACS Here is the input file: . . . pull_group0 = POPC pull_weights0= pull_pbcatom0= 0 pull_group1 = DNA pull_weights1= pull_pbcatom1= 0 pull_vec1= 0.0 0.0 0.0 pull_init1 = 0.0 0.0 0.0 pull_rate1 = 0 pull_k1 = 300 pull_kB1 = 200 free_energy = yes restraint-lambdas = 1.0 0.5 0.0 init-lambda-state = 0 nstdhdl = 10 . . . Any idea about it? Thanks, Parisa -- View this message in context: http://gromacs.5086.x6.nabble.com/window-exchange-umbrella-sampling-tp5009894p5009899.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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 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 convert a cpt file to an old version of gromacs
Dear Gromacs users, Can anyone please help me how can I convert a cpt file from a new to an older Gromacs version? Thanks -- 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] extraction of PDB from clusters.pdb
Sir, Using g_cluster I clustered snapshots in md trajectory using the command as follows g_cluster -s sd_7.tpr -f traj7.trr -dist rmsd-distribution.xvg -o clusters.xpm -sz cluster-sizes.xvg -tr cluster-transitions.xpm -ntr cluster-transitions.xvg -clid cluster-id-over-time.xvg -cl clusters.pdb -cutoff 0.25 -method gromos -dt 10 Here I got clusters.pdb having central structures in each cluster. Is there any command line option available to extract all individual files from clusters.pdb. -- 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] TFE-water simulation
HI, I want to simulate helical peptide in TFE-water (1:1 vol) solvent. 1. From previous searches, I got to know that tfe.itp is present in gmx.ff folder. Can I use this itp file by including it in my top file generated during pdb2gmx. 2. I also got TFE-water (1:1 vol) pdb and gro pre-equilibrated system from ATB site. I dont know if I can use either this pdb or gro file during genbox step for -cs flag Can anyone help me out in this regard. Thanks in advance. Regards, Archana Sonawani-Jagtap Senior Research Fellow, Biomedical Informatics Centre, NIRRH (ICMR), Parel Mumbai, India. 9960791339 -- 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
