Re: [gmx-users] Bootstrap error
Hi, You don't need to compile the latest CMake on Ubuntu, you can use the version available in the apt package management system. But you will need a C++ compiler for recent versions of GROMACS, so get the latest gcc for your Ubuntu version while you are doing that. Mark On Mon, Apr 13, 2015 at 6:54 PM, su sun.i...@gmail.com wrote: Dear All I am new to Gromacs and i am trying to install it in Ubuntu. I am getting following error while using the command ./configure in cmake step. C compiler on this system is: cc Error when bootsratpping CMake: Cannot find appropriate C++ compiler on this system. Please specify one using environment varaible CXX. See cmake_bootsrap.log for compilers attempted Log of Errors: /home/user/Downloads/Cmake-3.2.1/Bootstrap.cmk/cmake_bootstrap.log Please Help Regards Suniba Sent from my iPhone -- 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] about GPU acceleration
Yes. -- Szilárd On Fri, Apr 10, 2015 at 12:42 PM, BIRD vgsplay...@163.com wrote: Dear all Does the new Gromacs5 support the SHIFT for Lennard Jones and Coulombic interactions by GPU acceleration? thank you Cao Ph.D Nankai University Tianjin China -- 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] Clusters
Are there any tutorial or tips to use cluster in Gromacs? I have 5 nodes with 9 cores each node and want use all them in one simulation, is that possible? I've read something about gromacs MPI but I don't know how to use. Can someone suggest some text or some tutorial for me? Thanks in advance, Lucas -- 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 call an external LAPACK function in gromacs
Dear All, I am a new user of gromacs 5.0. For my own purposes I made small changes in a gromacs source code where I called a function named DPOTRF. This is a standard function in LAPACK library but not in the gromacs internal LAPACK library. Now I have a problem of compiling. What I did is: cmake .. -DGMX_EXTERNAL_BLAS=on -DGMX_EXTERNAL_LAPACK=on -DCMAKE_PREFIX_PATH=/usr/lib64 (this is the path of my extenal LAPACK library) this step is ok but next when I make, the error I got is: Linking CXX executable ../../bin/template ../../lib/libgromacs.so.0.0.0: undefined reference to `dpotrf' collect2: error: ld returned 1 exit status make[2]: *** [bin/template] Error 1 make[1]: *** [share/template/CMakeFiles/template.dir/all] Error 2 Could anyone help me with this problem? Thanks a lot. Sincerely, Qian -- 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] Clusters
What network do you have? Unless it's fast (that is low latency) you won't be able to run across nodes. Are you sure about 9 cores, that number seems strange? -- Szilárd On Mon, Apr 13, 2015 at 11:52 PM, Lucas Dadalt Morero ld...@hotmail.com wrote: Are there any tutorial or tips to use cluster in Gromacs? I have 5 nodes with 9 cores each node and want use all them in one simulation, is that possible? I've read something about gromacs MPI but I don't know how to use. Can someone suggest some text or some tutorial for me? Thanks in advance, Lucas -- 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] Clusters
Sorry, it's 8 cores. Network is good. The hardware setup is ok, I just want to know how to perform a gromacs simulation using all the nodes.. Lucas Date: Tue, 14 Apr 2015 02:06:49 +0200 From: pall.szil...@gmail.com To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Clusters What network do you have? Unless it's fast (that is low latency) you won't be able to run across nodes. Are you sure about 9 cores, that number seems strange? -- Szilárd On Mon, Apr 13, 2015 at 11:52 PM, Lucas Dadalt Morero ld...@hotmail.com wrote: Are there any tutorial or tips to use cluster in Gromacs? I have 5 nodes with 9 cores each node and want use all them in one simulation, is that possible? I've read something about gromacs MPI but I don't know how to use. Can someone suggest some text or some tutorial for me? Thanks in advance, Lucas -- 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. -- 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] POPE lipid from Tieleman's web site, the box of xy dimension will shrink during the simulation
Dear Thomas; Thanks for your suggestion. I will try for it. Sciences: Nie Xuechuan At 2015-04-12 04:34:18, Thomas Piggot t.pig...@soton.ac.uk wrote: Justin is right about the parameters being sub-optimal, for example see: de Vries et al. http://pubs.acs.org/doi/abs/10.1021/jp0366926 which I think was the first mention of issues with the 'Berger' PE parameters. There are plenty of force fields out there for PE membranes (both all-atom and united-atom) which do a much better job. If you really really want to use Berger you can use the fudge as mentioned in this paper to include some repulse LJ interactions on the headgroup hydrogens. From some tests I did ages ago, I think you need a larger repulsive force than is mentioned in the paper (which uses DOPE) to get POPE to behave sensibly (IIRC). Cheers Tom On 11/04/15 21:09, Justin Lemkul wrote: On 4/11/15 8:25 AM, niexuechuan wrote: Dear all, I am new to lipid simulation. I have downloaded the pope.pdb, pope.itp, lipid.itp from Tieleman's web site (http://wcm.ucalgary.ca/tieleman/downloads). And I have made a directory named gromos53a6_lipid.ff followed Justin's tutorial (http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/index.html). Then I use pope.pdp to run a pure 340 POPE lipid MD at 310K. But I find that the box of xy dimension will shrink from 9.6nm*9.5nm to 9.0nm*8.9nm after 20 ns, then it fluctuates at that value till 200ns. The box of z dimension will increase a little to hold the volume constant. This will lead to the area per lipid decreased from 0.54 nm^2 to 0.47nm^2. At the same time, I find the order parameter of lipid tail (Scd) is too big (above 0.3). Does any one know where the problem is? This could very well be due to suboptimal parameters. Has anyone ever verified that these POPE parameters produce APL and order parameters in agreement with experimental values over such long time frames? Lipid force fields are very sensitive and not all parameter sets are created equal. -Justin When I use dppc128.pdb from Tieleman's web site to run a pure DPPC lipid MDat 323K, the box will not shrink. And the area per lipid of DPPC is in accordance with literature, about 0.62nm^2. The water model is SPC. My mdp file is also from Justin's tutorial. Followed is my mdp file of POPE: title= KALP15-DPPC Production MD ; Run parameters integrator= md; leap-frog integrator nsteps= 1; 2 * 50 = 1000 ps (1 ns) dt = 0.002; 2 fs ; Output control nstxout= 0; save coordinates every 2 ps nstvout= 0; save velocities every 2 ps nstxtcout= 1000; xtc compressed trajectory output every 2 ps nstenergy= 1000; save energies every 2 ps nstlog= 1000; update log file every 2 ps ; Bond parameters continuation= yes; Restarting after NPT 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 cels nstlist= 5; 10 fs rlist= 1.2; short-range neighborlist cutoff (in nm) 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 fourierspacing= 0.16; grid spacing for FFT ; Temperature coupling is on tcoupl= Nose-Hoover; More accurate thermostat tc-grps= POPE SOL;SOL_CL; three coupling groups - more accurate tau_t= 0.50.5;0.5; time constant, in ps ref_t= 310 310;323; reference temperature, one for each group, in K ; Pressure coupling is on pcoupl= Parrinello-Rahman; Pressure coupling on in NPT pcoupltype= semiisotropic; uniform scaling of x-y box vectors, independent z tau_p= 2.0; time constant, in ps ref_p= 1.01.0; reference pressure, x-y, z (in bar) compressibility = 4.5e-54.5e-5; isothermal compressibility, 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; Velocity generation is off ; COM motion removal ; These options remove motion of the protein/bilayer relative to the solvent/ions nstcomm = 1 comm-mode = Linear comm-grps = POPE SOL ; Scale COM of reference coordinates (when postion restraint) ;refcoord_scaling = com And my topol file: #include gromos53a6_lipid.ff/forcefield.itp #include pope.itp ; Include water topology #include gromos53a6_lipid.ff/spc.itp ; System specifications [ system ] 340-Lipid POPE and CNP [ molecules ] ; molecule name nr. POPE 340 SOL 6729 Thanks in advance, Nie Xuechuan Shanghai Institute of Applied Physics, Chinese Academy of Sciences -- Dr Thomas
Re: [gmx-users] POPE lipid from Tieleman's web site, the box of xy dimension will shrink during the simulation
Dear Justin; Thanks for your reply! Maybe I will use other kind of lipid or force field instead. Sciences: Nie Xuechuan At 2015-04-12 04:09:24, Justin Lemkul jalem...@vt.edu wrote: On 4/11/15 8:25 AM, niexuechuan wrote: Dear all, I am new to lipid simulation. I have downloaded the pope.pdb, pope.itp, lipid.itp from Tieleman's web site (http://wcm.ucalgary.ca/tieleman/downloads). And I have made a directory named gromos53a6_lipid.ff followed Justin's tutorial (http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/index.html). Then I use pope.pdp to run a pure 340 POPE lipid MD at 310K. But I find that the box of xy dimension will shrink from 9.6nm*9.5nm to 9.0nm*8.9nm after 20 ns, then it fluctuates at that value till 200ns. The box of z dimension will increase a little to hold the volume constant. This will lead to the area per lipid decreased from 0.54 nm^2 to 0.47nm^2. At the same time, I find the order parameter of lipid tail (Scd) is too big (above 0.3). Does any one know where the problem is? This could very well be due to suboptimal parameters. Has anyone ever verified that these POPE parameters produce APL and order parameters in agreement with experimental values over such long time frames? Lipid force fields are very sensitive and not all parameter sets are created equal. -Justin When I use dppc128.pdb from Tieleman's web site to run a pure DPPC lipid MDat 323K, the box will not shrink. And the area per lipid of DPPC is in accordance with literature, about 0.62nm^2. The water model is SPC. My mdp file is also from Justin's tutorial. Followed is my mdp file of POPE: title= KALP15-DPPC Production MD ; Run parameters integrator= md; leap-frog integrator nsteps= 1; 2 * 50 = 1000 ps (1 ns) dt= 0.002; 2 fs ; Output control nstxout= 0; save coordinates every 2 ps nstvout= 0; save velocities every 2 ps nstxtcout= 1000; xtc compressed trajectory output every 2 ps nstenergy= 1000; save energies every 2 ps nstlog= 1000; update log file every 2 ps ; Bond parameters continuation= yes; Restarting after NPT 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 cels nstlist= 5; 10 fs rlist= 1.2; short-range neighborlist cutoff (in nm) 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 fourierspacing= 0.16; grid spacing for FFT ; Temperature coupling is on tcoupl= Nose-Hoover; More accurate thermostat tc-grps= POPE SOL;SOL_CL; three coupling groups - more accurate tau_t= 0.50.5;0.5; time constant, in ps ref_t= 310 310;323; reference temperature, one for each group, in K ; Pressure coupling is on pcoupl= Parrinello-Rahman; Pressure coupling on in NPT pcoupltype= semiisotropic; uniform scaling of x-y box vectors, independent z tau_p= 2.0; time constant, in ps ref_p= 1.01.0; reference pressure, x-y, z (in bar) compressibility = 4.5e-54.5e-5; isothermal compressibility, 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; Velocity generation is off ; COM motion removal ; These options remove motion of the protein/bilayer relative to the solvent/ions nstcomm = 1 comm-mode = Linear comm-grps = POPE SOL ; Scale COM of reference coordinates (when postion restraint) ;refcoord_scaling = com And my topol file: #include gromos53a6_lipid.ff/forcefield.itp #include pope.itp ; Include water topology #include gromos53a6_lipid.ff/spc.itp ; System specifications [ system ] 340-Lipid POPE and CNP [ molecules ] ; molecule name nr. POPE 340 SOL 6729 Thanks in advance, Nie Xuechuan Shanghai Institute of Applied Physics, Chinese Academy of Sciences -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to
Re: [gmx-users] Number of hardware threads does not match OpenMP
Hi, The former warning is the direct consequence of the latter. Your job scheduler or MPI launcher is setting process affinity; as a result the OpenMP library reports 1 CPU in contrast with the 20 CPUs/cores that our low-level detection reports. You could be loosing a considerable amount of performance if the thread affinity you set/get is not the correct/suitable one - my guess is that it likely is, consecutive ranks are likely pinned to consecutive cores. You can try either disabling the affinity setting in PBS or using some MPI environment variable or override it with the -pin on mdrun argument. Cheers, -- Szilárd On Fri, Apr 10, 2015 at 8:09 PM, Dries Van Rompaey dries.vanromp...@gmail.com wrote: Dear all, When running a simulation of a protein in solution on my university’s cluster I get the two following notifications: Number of hardware threads detected (20) does not match the number reported by OpenMP (1). Consider setting the launch configuration manually! Non-default thread affinity set probably by the OpenMP library, disabling internal thread affinity. My PBS file is: #!/bin/bash #PBS -l nodes=2:ppn=20,pmem=2gb #PBS -l walltime=55:00:00 #PBS -N GromacsmTSLP module load hopper/2015a module load GROMACS/5.0.4-intel-2015a-hybrid cd $PBS_O_WORKDIR mpirun gmx_mpi mdrun -s md_calcua.tpr -o $VSC_DATA/MD.trr -cpo $VSC_DATA/MD.cpt -c $VSC_DATA/MD.gro -e $VSC_DATA/MD.edr -g $VSC_DATA/MD.log The performance of the system seems to be allright (120 ns/day on 2 Xeon E5-2680 v2 @ 2.80GHz, 20 000 atoms). The number of processes launched seems to be correct as well (40). I tried looking through the mailing list, and from what I can gather these notifications should only have an effect on the system performance (which seems to be okay in my case)? Am I correct in thinking this won’t affect the results from my simulations? Thanks in advance Dries -- 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] CNT force field and simulation
Hi Pierre, Two things: 1. rtp entries are pretty useless for crystal structures. Biochemical simulations use molecules with a precise atomic composition, so an rtp template makes sense. Not for crystals. Your rtp entry contains useless information and the only thing in your coordinates that can fit that template is one atom, which is already generous. So, you get one atom in your GRO. ;) 2. Andrea isn't using pdb2gmx, which relies on templates. I honestly have no idea why he created that rtp entry, so maybe other users will clarify that. Andrea uses x2top, which will look up data in ffbonded, ffnonbonded, and in atomname to type translator. This is the right way to treat crystals in GMX. Moreover, you will have to do that every time you have a new set of coordinates. Use what he uses and you won't get any new GRO files. All you will get is a topology to go with your original PDB -- and that is all you need to run a simulation. Alex On Mon, Apr 13, 2015 at 5:49 PM, Pierre Bertin bertin...@gmail.com wrote: Hi Alex, All right, I red all this weekend and I know how to modify a force field to add residues (I hope... ahah). I modified OPLSAA force field because I want to add a protein to my CNT. So, I have edited these files with Andrea Minoia datas (and yours) : *aminoacids.rtp* : [ CNT ] 39 [ atoms ] 40 SWTSWT0 2 41 SWTSWT0 3 42 [ bonds ] 43SWT SWT SWT 44SWT SWT I added a new residue named CNT. 2 or 3 bonds, I do not include hydrogen to start. So a carbon can have 2 (extremities) or 3 bonds (internal). *atomname2type.n2t :* 24 CSWT 0 12.011 2SWT 0.142 SWT 0.142 25 CSWT 0 12.011 3SWT 0.142 SWT 0.142 SWT 0.142 Here, conversion of C atoms from CNT.pdb file to SWT new atom type. *atomtypes.atp :* 823 SWT12.01100 ;CNT Here, define the new atom type : SWT with the carbon mass. *ffbonded.itp : * [ bonds ] SWT SWT 10.1420420420.0 ; CNT SWT SWT bond is a bond between 2 carbons in CNT. I have used your data Alex. [ angletype ] SWTSWTSWT 1 120.000659.346 ; CNT Angle type between the 3 atoms of carbon with datas from you email and the same in dihedral with : [ dihedraltypes ] SWTSWTSWTSWT 3 17.30770 0.0 -17.30770 0.0 0.0 0.0 ; CNT I have tried with SWT, with C and in n2t with a reference to oplsaa carbon from benzene. This works, I can build the .gro file with : gmx pdb2gmx -f cnt_gro.pdb -o cnt_gro.gro -p cnt_gro.top And then I select OPLSAA force field and TIP3P for water. Problem : My cnt_gro.gro has only ONE atom of carbon. And I do not have error message. What did I do wrong? Thanks you a lot for your consideration and time. I attach the pdb file. *Pierre BERTIN* Bioinformatics and Biostatistics student (MSc), University Paris-Sud XI, ORSAY. 2015-04-11 14:31 GMT-06:00 Alex nedoma...@gmail.com: Great, glad it's working. I think there was a wrong bond length somewhere in Andrea's tutorial, not sure where exactly (I could be wrong). Look at everything carefully and make sure the bond lengths are at 0.142 nm, because this is what the generator is doing. Have fun! Alex Thank you a lot, I did this and exactly as you are saying I do not have the message. I use the link posted in my first message : ( http://www.nanotube.msu.edu/tubeASP/) And then, I converted with Babel. But I removed CONECT statements. And now I am modifying files as you said and trying to run the tutorial. Thank you a lot Alex! -- 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] CNT force field and simulation
Also, I would really suggest that you read the Gromacs manual on the subject of topology. This is extremely useful, because there is a philosophical clash between biomolecular simulations and solid-state simulations in terms of the concept of connectivity. You are effectively using a tool that is broadly inappropriate for solid-state systems. So, understanding the concept of topology in GMX-like packages is extremely useful. Gromacs has a manual of outstanding quality, and it should become your Holy Bible. :) Alex On Mon, Apr 13, 2015 at 6:31 PM, Alex nedoma...@gmail.com wrote: Hi Pierre, Two things: 1. rtp entries are pretty useless for crystal structures. Biochemical simulations use molecules with a precise atomic composition, so an rtp template makes sense. Not for crystals. Your rtp entry contains useless information and the only thing in your coordinates that can fit that template is one atom, which is already generous. So, you get one atom in your GRO. ;) 2. Andrea isn't using pdb2gmx, which relies on templates. I honestly have no idea why he created that rtp entry, so maybe other users will clarify that. Andrea uses x2top, which will look up data in ffbonded, ffnonbonded, and in atomname to type translator. This is the right way to treat crystals in GMX. Moreover, you will have to do that every time you have a new set of coordinates. Use what he uses and you won't get any new GRO files. All you will get is a topology to go with your original PDB -- and that is all you need to run a simulation. Alex On Mon, Apr 13, 2015 at 5:49 PM, Pierre Bertin bertin...@gmail.com wrote: Hi Alex, All right, I red all this weekend and I know how to modify a force field to add residues (I hope... ahah). I modified OPLSAA force field because I want to add a protein to my CNT. So, I have edited these files with Andrea Minoia datas (and yours) : *aminoacids.rtp* : [ CNT ] 39 [ atoms ] 40 SWTSWT0 2 41 SWTSWT0 3 42 [ bonds ] 43SWT SWT SWT 44SWT SWT I added a new residue named CNT. 2 or 3 bonds, I do not include hydrogen to start. So a carbon can have 2 (extremities) or 3 bonds (internal). *atomname2type.n2t :* 24 CSWT 0 12.011 2SWT 0.142 SWT 0.142 25 CSWT 0 12.011 3SWT 0.142 SWT 0.142 SWT 0.142 Here, conversion of C atoms from CNT.pdb file to SWT new atom type. *atomtypes.atp :* 823 SWT12.01100 ;CNT Here, define the new atom type : SWT with the carbon mass. *ffbonded.itp : * [ bonds ] SWT SWT 10.1420420420.0 ; CNT SWT SWT bond is a bond between 2 carbons in CNT. I have used your data Alex. [ angletype ] SWTSWTSWT 1 120.000659.346 ; CNT Angle type between the 3 atoms of carbon with datas from you email and the same in dihedral with : [ dihedraltypes ] SWTSWTSWTSWT 3 17.30770 0.0 -17.30770 0.0 0.0 0.0 ; CNT I have tried with SWT, with C and in n2t with a reference to oplsaa carbon from benzene. This works, I can build the .gro file with : gmx pdb2gmx -f cnt_gro.pdb -o cnt_gro.gro -p cnt_gro.top And then I select OPLSAA force field and TIP3P for water. Problem : My cnt_gro.gro has only ONE atom of carbon. And I do not have error message. What did I do wrong? Thanks you a lot for your consideration and time. I attach the pdb file. *Pierre BERTIN* Bioinformatics and Biostatistics student (MSc), University Paris-Sud XI, ORSAY. 2015-04-11 14:31 GMT-06:00 Alex nedoma...@gmail.com: Great, glad it's working. I think there was a wrong bond length somewhere in Andrea's tutorial, not sure where exactly (I could be wrong). Look at everything carefully and make sure the bond lengths are at 0.142 nm, because this is what the generator is doing. Have fun! Alex Thank you a lot, I did this and exactly as you are saying I do not have the message. I use the link posted in my first message : ( http://www.nanotube.msu.edu/tubeASP/) And then, I converted with Babel. But I removed CONECT statements. And now I am modifying files as you said and trying to run the tutorial. Thank you a lot Alex! -- 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] A simple question
Dear Dr.Smith , Thanks for your replay . This is a part of my PDB file : ATOM 1 CD1 TRP 1 19.910 19.430 16.500 1.00 0.00ATOM 2 CD1 TRP 1 20.210 20.850 16.560 1.00 0.00ATOM 3 CD1 TRP 1 19.010 21.540 16.970 1.00 0.00ATOM 4 CD1 TRP 1 17.960 20.560 17.150 1.00 0.00ATOM 5 CD1 TRP 1 18.520 19.250 16.860 1.00 0.00ATOM 6 CD1 TRP 1 19.090 22.640 17.820 1.00 0.00...I want to define C-delta atom of the aromatic tryptophan amino acid for C60 carbons and i want to use oplsaa force field. Best regards ,Saeed. From: Smith, Micholas D. smit...@ornl.gov To: gmx-us...@gromacs.org gmx-us...@gromacs.org; saeed poorasad s_poora...@yahoo.com Sent: Monday, 13 April 2015, 21:24 Subject: Re: [gmx-users] A simple question Hi Saeed, Attachments don't work with the mailing list. Could you copy a few lines of the pdb for us to look at and maybe upload the pdb you generated to dropbox or a similar site? Also pdb2gmx may not be the best route here. You may need to explicitly write your own topology file (tedious as it may be), but lets take a closer look at what your pdb first. === Micholas Dean Smith, PhD. Post-doctoral Research Associate University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of saeed poorasad s_poora...@yahoo.com Sent: Monday, April 13, 2015 2:29 AM To: gmx-us...@gromacs.org Subject: [gmx-users] A simple question Hi . Dear Gromacs users . Today is the first day that i am working with GROMACS .I want to have a system with one C60 and about 1000 water molecules .I tried to use pdb2gmx on C60.pdb but I got fatal error , I think the problem is because of my PDB file .I want to define C-delta atom of the aromatic tryptophan amino acid for C60 carbons and i want to use oplsaa force field. Can you please let me know what the problem is ? I have attached my PDB file with this Email. Best ,Saeed. -- 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] Post-Processing on the REMD trj
Dear users, Rescently, I used REMD to do some simulation by Gromacs , I konw GROMACS exchanges coordinates. So does this means every trajectory was written at a temperture ?AND if i want to analyse the lowest temperature, can I just analyse md0.xtc as 'trajectory no longer be continuous'(http://www.gromacs.org/Documentation/Tutorials/GROMACS_USA_Workshop_and_Conference_2013/An_introduction_to_replica_exchange_simulations:_Mark_Abraham,_Session_1B)? secondly， the Perl script demux.pl can analyse a single REMD .log file and writes two special .xvg files .But i got some problem ,as we can see blow , 0 012345678 4 012345678 8 012345687 12 012435687 16 012435687 20 012436587 24 021435678 28 021435678 32 021435678 36 021435678 40 021435678 44 021345678 48 021345678 52 012435678 56 012435678 60 021345678 64 012345687 68 012345687 72 012345687 76 012345687 the 0 didn't exchange ,however the log describes the 0 did exchange . i think my log produced by gromacs4.6.5 doesn't match the Perl script demux.pl. Can someone tell me how to modify the Perl script demux.pl.? thank you Dongdong Wang -- Dongdong Wang Chemistry Department Fudan University 200433, Shanghai P.R. China Tel:+86 15121115863 Email: 14110220...@fudan.edu.cn -- 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] Bootstrap error
Thank you very much. Sent from my iPhone On 13-Apr-2015, at 11:24 pm, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, You don't need to compile the latest CMake on Ubuntu, you can use the version available in the apt package management system. But you will need a C++ compiler for recent versions of GROMACS, so get the latest gcc for your Ubuntu version while you are doing that. Mark On Mon, Apr 13, 2015 at 6:54 PM, su sun.i...@gmail.com wrote: Dear All I am new to Gromacs and i am trying to install it in Ubuntu. I am getting following error while using the command ./configure in cmake step. C compiler on this system is: cc Error when bootsratpping CMake: Cannot find appropriate C++ compiler on this system. Please specify one using environment varaible CXX. See cmake_bootsrap.log for compilers attempted Log of Errors: /home/user/Downloads/Cmake-3.2.1/Bootstrap.cmk/cmake_bootstrap.log Please Help Regards Suniba Sent from my iPhone -- 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. -- 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] A query
Thank you all for the reply. On Mon, Apr 13, 2015 at 6:39 PM, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, Yes, there are a few programs in computational chemistry that give such quotes randomly; GAUSSIAN comes to mind. There's an environment variable described in one of the manual appendices that will disable them, if you prefer. Mark On 13/04/2015 12:25 pm, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Priya, Yes, this particular message means that you should also get to know yourself, because it is key to understand others, which is the most important step to not being lonely. This one may not be directly related to the program, but in terms of science, it sort of suggests that you should not use research as escapism to avoid researching yourself. There's something out there too. The messages are many, and range from philosophical to literary MD references to 'noteworthy' Gromacs' developer quotes. Cheers, Tsjerk On Mon, Apr 13, 2015 at 12:04 PM, Priya Das priyadas...@gmail.com wrote: Dear All, *gcq#6: It's So Lonely When You Don't Even Know Yourself (Red Hot Chili Peppers)* Such messages pop up after running the gromacs commands on terminal. Do these messages have any meaning ? Have they anything to do with the programs we are running? -- *Let us all join hands to save our Mother Earth* Regards, Priya Das Research Scholar Dept. of Computational Biology and Bioinformatics, University of Kerala -- 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. -- Tsjerk A. Wassenaar, Ph.D. -- 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. -- *Let us all join hands to save our Mother Earth* Regards, Priya Das Research Scholar Dept. of Computational Biology and Bioinformatics, University of Kerala -- 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] generating full atomic structure
Dear all, I got a pdb file including the C-alpha itoms of different residues only. Is there any software that can add the other atoms of the residues to the pdb file automatically? Thanks in advance, Ming -- 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] A simple question
Hi . Dear Gromacs users . Today is the first day that i am working with GROMACS .I want to have a system with one C60 and about 1000 water molecules .I tried to use pdb2gmx on C60.pdb but I got fatal error , I think the problem is because of my PDB file .I want to define C-delta atom of the aromatic tryptophan amino acid for C60 carbons and i want to use oplsaa force field. Can you please let me know what the problem is ? I have attached my PDB file with this Email. Best ,Saeed.-- 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] A query
Dear All, *gcq#6: It's So Lonely When You Don't Even Know Yourself (Red Hot Chili Peppers)* Such messages pop up after running the gromacs commands on terminal. Do these messages have any meaning ? Have they anything to do with the programs we are running? -- *Let us all join hands to save our Mother Earth* Regards, Priya Das Research Scholar Dept. of Computational Biology and Bioinformatics, University of Kerala -- 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] A query
Hi Priya, Yes, this particular message means that you should also get to know yourself, because it is key to understand others, which is the most important step to not being lonely. This one may not be directly related to the program, but in terms of science, it sort of suggests that you should not use research as escapism to avoid researching yourself. There's something out there too. The messages are many, and range from philosophical to literary MD references to 'noteworthy' Gromacs' developer quotes. Cheers, Tsjerk On Mon, Apr 13, 2015 at 12:04 PM, Priya Das priyadas...@gmail.com wrote: Dear All, *gcq#6: It's So Lonely When You Don't Even Know Yourself (Red Hot Chili Peppers)* Such messages pop up after running the gromacs commands on terminal. Do these messages have any meaning ? Have they anything to do with the programs we are running? -- *Let us all join hands to save our Mother Earth* Regards, Priya Das Research Scholar Dept. of Computational Biology and Bioinformatics, University of Kerala -- 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. -- Tsjerk A. Wassenaar, Ph.D. -- 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] A query
Nope! They are just for our amusement. Maybe only one has to do it: Check your input! David van der Spoel Cheers! Marcelo Depólo Em 13/04/2015 07:05, Priya Das priyadas...@gmail.com escreveu: Dear All, *gcq#6: It's So Lonely When You Don't Even Know Yourself (Red Hot Chili Peppers)* Such messages pop up after running the gromacs commands on terminal. Do these messages have any meaning ? Have they anything to do with the programs we are running? -- *Let us all join hands to save our Mother Earth* Regards, Priya Das Research Scholar Dept. of Computational Biology and Bioinformatics, University of Kerala -- 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] how to modify the files in the force field fold of Gromacs
Dear all, I need to modify the .rtp file in charmm27.ff, but I can do nothing. How to change the access to those files? Thanks in advance, Ming -- 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 modify the files in the force field fold of Gromacs
Hi Ming, Copy the whole folder to your working directory. Gromacs will give force field files in the working directory precedence. Cheers, Tsjerk On Mon, Apr 13, 2015 at 12:32 PM, Ming Tang m21.t...@qut.edu.au wrote: Dear all, I need to modify the .rtp file in charmm27.ff, but I can do nothing. How to change the access to those files? Thanks in advance, Ming -- 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. -- Tsjerk A. Wassenaar, Ph.D. -- 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] Can NAMD simulation solve the problem of coordinate clash in a structural model?
Hi Yeping Sun, If the coordinates are garbled (what are serious coordinate clashes?), you'll have a hard time with either NAMD or Gromacs. Cheers, Tsjerk On Mon, Apr 13, 2015 at 6:05 AM, sunyeping sunyep...@aliyun.com wrote: Dear all, I modelled a structural model of a complex containing two large proteins. There are serious coordinate clashes between these two proteins in the model. Can I expect to do Gromacs simulation to solve the problem of cooridnate clash and obtain a more rational model? Best regards, Yeping Sun Institute of Microbiology, Chinese Academy of Sciences -- 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. -- Tsjerk A. Wassenaar, Ph.D. -- 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 add a repulsive harmonic potential
On 4/12/15 10:40 PM, atsutoshi.ok...@takeda.com wrote: Thank you for your help. Actually, I want to predict the binding mode of ligand for protein/ligand complex during long time simulation, so I want to add only repulsive potential between ligands to avoid ligand aggregation, not fix these ligands. The reason why I add some ligand molecules(not one ligand) in simulation is to enhance ligand sampling. I tried using [distance_restaints] below, not use [bonds] because of domain decomposition error. Then, the MD simulation could run normally without domain decomposition error! [ distance_restraints ] ;ai aj type index type' low up1 up2 fac 13 63 11 120 100 100 1 However, the distance between 13 atom and 63 atom seems to be less than 20 angstrom in every steps of MD simulation. So I tried to change the fac value from 1 to -1, but the distance was less than 20 angstrom during MD simulation Why the ligands were restrained less than 20 angstrom although I think I add repulsive force between these atoms? Depending on how structurally complex the ligands are, it may be very easy to define a dummy atom within the structure using a virtual site, then specifying a nonbonded interaction only between these virtual sites using [nonbond_params]. That way, these sites will not affect ligand-water, ligand-protein, etc but will repel ligands from one another. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] How to add a repulsive harmonic potential
Hi, For distance restraints, there is also an mdp section in which you must choose values. Mark On 13/04/2015 4:42 am, atsutoshi.ok...@takeda.com wrote: Thank you for your help. Actually, I want to predict the binding mode of ligand for protein/ligand complex during long time simulation, so I want to add only repulsive potential between ligands to avoid ligand aggregation, not fix these ligands. The reason why I add some ligand molecules(not one ligand) in simulation is to enhance ligand sampling. I tried using [distance_restaints] below, not use [bonds] because of domain decomposition error. Then, the MD simulation could run normally without domain decomposition error! [ distance_restraints ] ;ai aj type index type' low up1 up2 fac 13 63 11 120 100 100 1 However, the distance between 13 atom and 63 atom seems to be less than 20 angstrom in every steps of MD simulation. So I tried to change the fac value from 1 to -1, but the distance was less than 20 angstrom during MD simulation Why the ligands were restrained less than 20 angstrom although I think I add repulsive force between these atoms? Bests regards, Atsutoshi Okabe Hi, If it's physical, then trying to suppress it arbitrarily does not seem likely to lead to useful observations. If it's an unphysical artefact of the model, then fixing the model seems more appropriate. Mark On Tue, Apr 7, 2015 at 7:35 AM, atsutoshi.ok...@takeda.com wrote: Thanks, Mark. So, do you have any good idea to avoid ligand aggregation in current released code? Best, Atsutoshi Okabe Hi, It seems like this is not a good idea after all. Things under a weak repulsive potential will move further away and run into such problems, because the domain decomposition needs to divide space geometrically. Mark On Mon, Apr 6, 2015 at 11:19 AM, atsutoshi.ok...@takeda.com wrote: Hi Mark, Thank you for your help. I use distance restraint implemented with [bonds] type 10 in current released code. [bonds] 13 63 10 2 9 9 41.8 However, I got the error message below. Fatal error: 1 of the 126679 bonded interactions could not be calculated because some atoms involved moved further apart than the multi-body cut-off distance (0.868598 nm) or the two-body cut-off distance (1.433 nm), see option -rdd, for pairs and tabulated bonds also see option -ddcheck I think this is the reason why is that the distance between restraint atoms of ligands to avoid aggregation is over two-body cut-off distance(1.433nm). The box size of simulation is 9.2*9.2*9.2(nM^3), so it is possible to be over the cut-off value because the distance is the inter-moleculer distance between ligands avoided aggregation. Could you advice how I can solve this error? Bests, Atsutoshi Okabe You can use a distance restraint (see manual) implemented with [bonds] type 10. In current released code, the atoms need to be within the same [moleculetype], which would likely mean you need to aggregate the ligands' topology definitions so that you can refer to atoms in different actual molecules that are now within the same [moleculetype] Alternatively, there is draft code for inter-molecular bonded interactions at https://gerrit.gromacs.org/#/c/2566/, but nobody has yet tried that it works. Mark On Fri, Nov 14, 2014 at 10:45 AM, atsutoshi.ok...@takeda.com wrote: Dear all To avoid ligand aggregation under higher concentration, I would like to introduce a weak repulsive potential term between the specific(e.g nitrogen) atoms of ligand molecules in the Protein/Ligand/Water system. This potential set as below. U(R) = K(R-R0)^2, if RR0 (repulsive potential) U(R) = 0, if RR0 Could you tell me how to add the repulsive harmonic potential in MD simulation? Bests, Atsutoshi Okabe 化学研究所(B42F-4110) 岡部 篤俊 (内線：704019、外線：0466-32-2706） -- 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] A query
Hi, Yes, there are a few programs in computational chemistry that give such quotes randomly; GAUSSIAN comes to mind. There's an environment variable described in one of the manual appendices that will disable them, if you prefer. Mark On 13/04/2015 12:25 pm, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Priya, Yes, this particular message means that you should also get to know yourself, because it is key to understand others, which is the most important step to not being lonely. This one may not be directly related to the program, but in terms of science, it sort of suggests that you should not use research as escapism to avoid researching yourself. There's something out there too. The messages are many, and range from philosophical to literary MD references to 'noteworthy' Gromacs' developer quotes. Cheers, Tsjerk On Mon, Apr 13, 2015 at 12:04 PM, Priya Das priyadas...@gmail.com wrote: Dear All, *gcq#6: It's So Lonely When You Don't Even Know Yourself (Red Hot Chili Peppers)* Such messages pop up after running the gromacs commands on terminal. Do these messages have any meaning ? Have they anything to do with the programs we are running? -- *Let us all join hands to save our Mother Earth* Regards, Priya Das Research Scholar Dept. of Computational Biology and Bioinformatics, University of Kerala -- 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. -- Tsjerk A. Wassenaar, Ph.D. -- 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] Effect of hardware threads mismatch on simulation
Dear gmx-users, When running a simulation of a protein in solution on my university’s cluster I get the two following notifications: Number of hardware threads detected (20) does not match the number reported by OpenMP (1). Consider setting the launch configuration manually! Non-default thread affinity set probably by the OpenMP library, disabling internal thread affinity. My PBS file is: #!/bin/bash #PBS -l nodes=2:ppn=20,pmem=2gb #PBS -l walltime=55:00:00 #PBS -N GromacsmTSLP module load hopper/2015a module load GROMACS/5.0.4-intel-2015a-hybrid cd $PBS_O_WORKDIR mpirun gmx_mpi mdrun -s md_calcua.tpr -o $VSC_DATA/MD.trr -cpo $VSC_DATA/MD.cpt -c $VSC_DATA/MD.gro -e $VSC_DATA/MD.edr -g $VSC_DATA/MD.log The performance of the system seems to be allright (120 ns/day on 2 Xeon E5-2680 v2 @ 2.80GHz), 20 000 atoms). The number of processes launched seems to be correct as well (40). I tried looking through the mailing list, and from what I can gather these notifications should only have an effect on the system performance (which seems to be okay in my case)? Could anyone tell me if this has an effect on the reliability of my simulations or not? Thanks in advance Dries -- 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] refcoord-scaling without pressure coupling
Dear GMX users, If I set refcoord-scaling = com and also pcoupl = no, will that refcoord-scaling = com do anything (like introducing additional numerical error in a NVE simulation) ? 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] generating full atomic structure
Hi, There are some suggestions on the GROMACS website. Mark On 13/04/2015 9:01 am, Ming Tang m21.t...@qut.edu.au wrote: Dear all, I got a pdb file including the C-alpha itoms of different residues only. Is there any software that can add the other atoms of the residues to the pdb file automatically? Thanks in advance, Ming -- 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] In-Vacuo ligand only equilibration (Iris Nira Smith)
Thank you Justin for your insight to your previous response. I made adjustments to my equilibration .mdp file (below) to run as NVT in vacuo. Can you review and advise on corrections? eqb-nvt-invacuo.mdp ;Title = equilibration nvt (invacuo) ; define = -DFLEXIBLE ; ;Run parameters integrator = md ;Algorithm options dt = 0.002 ; timestep for integration nsteps = 5 ; Maximum number of steps to perform 100 ps comm_mode = angular ; remove center of mass translation and rotation around the center of mass comm-grps = system ; ;Bond parameters constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained constraint_algorithm = lincs; holonomic constraints linc_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; ;Output control nstxout = 1000 ; frequency to write coordinates to output trajectory 2 ps nstfout = 1000 ; frequency to write forces to output trajectory 2 ps nstvout = 1000 ; frequency to write velocities to output trajectory 2 ps nstxtcout = 1000 ; xtc compressed trajectory output every 2 ps nstlog = 1000 ; frequency to write energies to log 2 ps nstenergy = 1000 ; frequency to write energies to edr 2ps ; ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist = 0 ; Frequency to update the neighbor list and long range forces ns_type = simple rlist = 0 ; Cut-off for making neighbor list (short range forces) coulombtype = cut-off ; Treatment of long range electrostatic interactions vdwtype = cut-off rcoulomb = 0; long range electrostatic cut-off rvdw = 0; long range Van der Waals cut-off pbc = no; Periodic Boundary Conditions (yes/no) epsilon_rf = 0 ; ; V-rescale temperature coupling is on tcoupl = v-rescale tc-grps = system tau-t = 0.1 ref-t = 300 ; ; Pressure coupling is off Pcoupl = no ; ; Generate velocites is on gen_vel = yes gen_temp= 300 gen_seed= 952967 -Iris On Apr 13, 2015, at 8:09 AM, gromacs.org_gmx-users-requ...@maillist.sys.kth.se wrote: Send gromacs.org_gmx-users mailing list submissions to gromacs.org_gmx-users@maillist.sys.kth.se To subscribe or unsubscribe via the World Wide Web, visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or, via email, send a message with subject or body 'help' to gromacs.org_gmx-users-requ...@maillist.sys.kth.se You can reach the person managing the list at gromacs.org_gmx-users-ow...@maillist.sys.kth.se When replying, please edit your Subject line so it is more specific than Re: Contents of gromacs.org_gmx-users digest... Today's Topics: 1. Re: How to add a repulsive harmonic potential (Justin Lemkul) 2. Re: In-Vacuo ligand only equilibration (Justin Lemkul) 3. Re: A simple question (Justin Lemkul) 4. Re: How to add a repulsive harmonic potential (Mark Abraham) 5. Re: A query (Mark Abraham) -- On 4/13/15 12:38 AM, Iris Nira Smith wrote: Hello, I'm utilizing gromacs 4.6.3 to set up my md simulation to run a ligand-only invacuo (no water) system for 500 ps prior to running my protein-ligand complex to determine the stability of the ligand. I have successfully run an energy minimization with the em-invaco.mdp file below (in absence of periodicity and infinite cut-offs). When running the equilibration should it be broken up into 2 phases: phase 1-nvt, phase 2-npt or is nvt sufficient? You can't do NPT in vacuo with an infinite system. If so, should it also be done utilizing an implicit solvent model such as GBSA for both equilibration and production run (see also eqb-invacuo.mdp below)? Implicit solvent and vacuum are physically different. If your in vacuo run is only to assess topological stability, don't bother with implicit solvent, because that adds a layer of complexity that will make it hard to tell if there are any problems. Implicit models are very approximate. -Justin em-invacuo.mdp ; Parameters describing what to do, when to stop and what to save integrator = steep ; Algorithm options ; steep = steepest descent minimization ; MD = Leap Frog algorith for integrating Newton? equations of motion ) emtol = 10.0 ; Stop minimization when the Fmax 10 kJ/mol/nm. emstep = 0.01 ; Energy step size nsteps = 1 ; Maximum number of (minimization) steps to perform nstenergy = 10 ; Write energies to disk every nstenergy steps ; ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist = 0 ; Frequency to update the neighbor list and long range forces ns_type = simple ; Method to determine neighbor list (simple, grid) rlist = 0 ; Cut-off for making neighbor list (short range forces) coulombtype = cut-off ; Treatment of long range electrostatic
Re: [gmx-users] A simple question
Hi Saeed, Attachments don't work with the mailing list. Could you copy a few lines of the pdb for us to look at and maybe upload the pdb you generated to dropbox or a similar site? Also pdb2gmx may not be the best route here. You may need to explicitly write your own topology file (tedious as it may be), but lets take a closer look at what your pdb first. === Micholas Dean Smith, PhD. Post-doctoral Research Associate University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of saeed poorasad s_poora...@yahoo.com Sent: Monday, April 13, 2015 2:29 AM To: gmx-us...@gromacs.org Subject: [gmx-users] A simple question Hi . Dear Gromacs users . Today is the first day that i am working with GROMACS .I want to have a system with one C60 and about 1000 water molecules .I tried to use pdb2gmx on C60.pdb but I got fatal error , I think the problem is because of my PDB file .I want to define C-delta atom of the aromatic tryptophan amino acid for C60 carbons and i want to use oplsaa force field. Can you please let me know what the problem is ? I have attached my PDB file with this Email. Best ,Saeed. -- 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] A simple question
On 4/13/15 2:29 AM, saeed poorasad wrote: Hi . Dear Gromacs users . Today is the first day that i am working with GROMACS .I want to have a system with one C60 and about 1000 water molecules .I tried to use pdb2gmx on C60.pdb but I got fatal error , I think the problem is because of my PDB file .I want to define C-delta atom of the aromatic tryptophan amino acid for C60 carbons and i want to use oplsaa force field. Can you please let me know what the problem is ? pdb2gmx won't work. You need to use gmx x2top or find some other tool to build the topology. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] generating full atomic structure
if your file is missing only the hydrogens, openbabel can add them for you. If your file is missing heavier atoms, I don't know. Hope this helps Victor 2015-04-13 2:00 GMT-05:00 Ming Tang m21.t...@qut.edu.au: Dear all, I got a pdb file including the C-alpha itoms of different residues only. Is there any software that can add the other atoms of the residues to the pdb file automatically? Thanks in advance, Ming -- 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] refcoord-scaling without pressure coupling
On 4/13/15 9:44 AM, Johnny Lu wrote: Dear GMX users, If I set refcoord-scaling = com and also pcoupl = no, will that refcoord-scaling = com do anything (like introducing additional numerical error in a NVE simulation) ? No. The option is only relevant with pressure coupling. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] generating full atomic structure
Thanks. It contains alpha carbons only. Sent from my Huawei Mobile Victor Rosas Garcia rosas.vic...@gmail.com wrote: if your file is missing only the hydrogens, openbabel can add them for you. If your file is missing heavier atoms, I don't know. Hope this helps Victor 2015-04-13 2:00 GMT-05:00 Ming Tang m21.t...@qut.edu.au: Dear all, I got a pdb file including the C-alpha itoms of different residues only. Is there any software that can add the other atoms of the residues to the pdb file automatically? Thanks in advance, Ming -- 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. -- 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] In-Vacuo ligand only equilibration
On 4/13/15 12:38 AM, Iris Nira Smith wrote: Hello, I'm utilizing gromacs 4.6.3 to set up my md simulation to run a ligand-only invacuo (no water) system for 500 ps prior to running my protein-ligand complex to determine the stability of the ligand. I have successfully run an energy minimization with the em-invaco.mdp file below (in absence of periodicity and infinite cut-offs). When running the equilibration should it be broken up into 2 phases: phase 1-nvt, phase 2-npt or is nvt sufficient? You can't do NPT in vacuo with an infinite system. If so, should it also be done utilizing an implicit solvent model such as GBSA for both equilibration and production run (see also eqb-invacuo.mdp below)? Implicit solvent and vacuum are physically different. If your in vacuo run is only to assess topological stability, don't bother with implicit solvent, because that adds a layer of complexity that will make it hard to tell if there are any problems. Implicit models are very approximate. -Justin em-invacuo.mdp ; Parameters describing what to do, when to stop and what to save integrator = steep ; Algorithm options ; steep = steepest descent minimization ; MD = Leap Frog algorith for integrating Newtonś equations of motion ) emtol = 10.0 ; Stop minimization when the Fmax 10 kJ/mol/nm. emstep = 0.01 ; Energy step size nsteps = 1 ; Maximum number of (minimization) steps to perform nstenergy = 10 ; Write energies to disk every nstenergy steps ; ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist = 0 ; Frequency to update the neighbor list and long range forces ns_type = simple ; Method to determine neighbor list (simple, grid) rlist = 0 ; Cut-off for making neighbor list (short range forces) coulombtype = cut-off ; Treatment of long range electrostatic interactions rcoulomb = 0 ; long range electrostatic cut-off rvdw = 0 ; long range Van der Waals cut-off constraints = none ; Bond types to replace by constraints pbc = no ; Periodic Boundary Conditions (yes/no) eqb-invacuo.mdp define = -DFLEXIBLE constraints = none ; Bond types to replace by constraints integrator = md ;Algorithm options dt = 0.002 ; timestep for integration nsteps = 5 ; Maximum number of steps to perform 100 ps nstxout = 1000 ; frequency to write coordinates to output trajectory 2 ps nstfout = 1000 ; frequency to write forces to output trajectory 2 ps nstvout = 1000 ; frequency to write velocities to output trajectory 2 ps nstxtcout = 1000 nstlog = 1000 ; frequency to write energies to log 2 ps nstenergy = 1000 ; frequency to write energies to edr ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist = 0 ; Frequency to update the neighbor list and long range forces ns_type = simple rlist = 0 ; Cut-off for making neighbor list (short range forces) coulombtype = cut-off ; Treatment of long range electrostatic interactions vdwtype = cut-off rcoulomb = 0 ; long range electrostatic cut-off rvdw = 0 ; long range Van der Waals cut-off pbc = no ; Periodic Boundary Conditions (yes/no) epsilon_rf = 0 rgbradii = 0 comm_mode = angular comm-grps = system optimize_fft = yes ; ; V-rescale temperature coupling is on tcoupl = v-rescale tc-grps = system tau-t = 0.1 ref-t = 300 ; ; Pressure coupling is off Pcoupl = no ; ; Generate velocites is on gen_vel = yes gen_temp = 300 gen_seed = -1 ; ; Implicit solvent implicit_solvent = GBSA gb_algorithm = Still gb_epsilon_solvent = 80 sa_surface_tension = 2.25936 nstgbradii = 1 rgbradii = 0 ; [nm] Cut-off for the calculation of the Born radii. Currently must be equal to rlist sa_algorithm = Ace-approximation sa_surface_tension = -1 Best, Iris Nira Smith, Ph.D. Candidate Briggs Computational Biochemistry/Biophysics Laboratory University of Houston 402E Health Science Center Houston, TX 77204 A Carnegie-designated Tier One public research university Phone:281-726-0341 Email: irisnsm...@comcast.net connormichaellogsdon.blogspot.com -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Bootstrap error
Dear All I am new to Gromacs and i am trying to install it in Ubuntu. I am getting following error while using the command ./configure in cmake step. C compiler on this system is: cc Error when bootsratpping CMake: Cannot find appropriate C++ compiler on this system. Please specify one using environment varaible CXX. See cmake_bootsrap.log for compilers attempted Log of Errors: /home/user/Downloads/Cmake-3.2.1/Bootstrap.cmk/cmake_bootstrap.log Please Help Regards Suniba Sent from my iPhone -- 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.
