[gmx-users] pulling direction in Umbrella sampling
Dear Users, I am using umbrella sampling method for unwinding of a peptide from binding site. I have to pull peptide in -X (negative direction). Can anyone suggest me keyword for this purpose. Should I use pulling_dim = Y N N or have to define some other keywords. I will be thankful for every help. Thanking you in advance. Regards Kshatresh Dutta Dubey -- 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] Estimations of the drug's affinity
Dear Gromacs users! I wounder to know if it possible to simple estimate drug affinity by mean of MD simulation? As I know the drug's property is based on the free energy change of bound-unbound ligand. So It seems that Justin's tutorial (free energy calculations) might be usefull if it would not be so routine for the drugs ( in that workflow several coulombic-vdw interactions must be uncoupled). Is there any more easily way to perform such calculations for the typical small-drug compounds consisted of several non-covalent interactions with the receptors ? James -- 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] pulling direction in Umbrella sampling
On 4/14/13 2:09 AM, Kshatresh Dutta Dubey wrote: Dear Users, I am using umbrella sampling method for unwinding of a peptide from binding site. I have to pull peptide in -X (negative direction). Can anyone suggest me keyword for this purpose. Should I use pulling_dim = Y N N or have to define some other keywords. Set pull_rate1 0 or otherwise use a different pull_geometry that allows you to specify pull_vec1, which allows you to set positive and negative vectors. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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] Estimations of the drug's affinity
On 4/14/13 2:13 AM, James Starlight wrote: Dear Gromacs users! I wounder to know if it possible to simple estimate drug affinity by mean of MD simulation? As I know the drug's property is based on the free energy change of bound-unbound ligand. So It seems that Justin's tutorial (free energy calculations) might be usefull if it would not be so routine for the drugs ( in that workflow several coulombic-vdw interactions must be uncoupled). Is there any more easily way to perform such calculations for the typical small-drug compounds consisted of several non-covalent interactions with the receptors ? Free energy calculations require considerable effort. You can approach the task in a number of ways - FEP, BAR, TI, LIE, PMF, MM/PBSA, etc. There is a large body of literature detailing methods for such calculations. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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] Estimations of the drug's affinity
Justin, and what exactly method from that list could be most easily performed in gromacs for the estimation of the affinity of small mollecules to the membrane receptors? 2013/4/14 Justin Lemkul jalem...@vt.edu On 4/14/13 2:13 AM, James Starlight wrote: Dear Gromacs users! I wounder to know if it possible to simple estimate drug affinity by mean of MD simulation? As I know the drug's property is based on the free energy change of bound-unbound ligand. So It seems that Justin's tutorial (free energy calculations) might be usefull if it would not be so routine for the drugs ( in that workflow several coulombic-vdw interactions must be uncoupled). Is there any more easily way to perform such calculations for the typical small-drug compounds consisted of several non-covalent interactions with the receptors ? Free energy calculations require considerable effort. You can approach the task in a number of ways - FEP, BAR, TI, LIE, PMF, MM/PBSA, etc. There is a large body of literature detailing methods for such calculations. -Justin -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://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] Estimations of the drug's affinity
On 4/14/13 8:54 AM, James Starlight wrote: Justin, and what exactly method from that list could be most easily performed in gromacs for the estimation of the affinity of small mollecules to the membrane receptors? There is no universal answer to that question. Explore the literature; there is a vast amount of information available on such calculations. Proceed with whatever is feasible and most reasonable for your purposes. -Justin 2013/4/14 Justin Lemkul jalem...@vt.edu On 4/14/13 2:13 AM, James Starlight wrote: Dear Gromacs users! I wounder to know if it possible to simple estimate drug affinity by mean of MD simulation? As I know the drug's property is based on the free energy change of bound-unbound ligand. So It seems that Justin's tutorial (free energy calculations) might be usefull if it would not be so routine for the drugs ( in that workflow several coulombic-vdw interactions must be uncoupled). Is there any more easily way to perform such calculations for the typical small-drug compounds consisted of several non-covalent interactions with the receptors ? Free energy calculations require considerable effort. You can approach the task in a number of ways - FEP, BAR, TI, LIE, PMF, MM/PBSA, etc. There is a large body of literature detailing methods for such calculations. -Justin -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://www.gromacs.org/Support/Mailing_Lists -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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] binding energy calculation when appear this error: no distance restraints in topology
On 4/14/13 9:38 AM, fatemeh ramezani wrote: Dear all After simulation of gold-protein interaction, now I want to calculate binding energy of each residue to gold. but when I use g_energy command appear this error: No distance restraints in topology How can I calculate binding energy without running simulation again(because it takes about one week and I need this result as soon as possible) ? Please provide the exact command you used. There is no reason for g_energy to be reading a topology to extract this information. You can get so-called nonbonded interaction energies decomposed by energy group, but whether or not you can call this an actual binding energy is highly questionable. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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] binding energy calculation when appear this error: no distance restraints in topology
the command that I used is : g_energy -f md300.edr -s fws_md300.tpr -o energy.xvg -pairs pairs.xvg Fatemeh Ramezani From: Justin Lemkul jalem...@vt.edu To: fatemeh ramezani fr_...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Sunday, 14 April 2013, 21:15 Subject: Re: [gmx-users] binding energy calculation when appear this error: no distance restraints in topology On 4/14/13 9:38 AM, fatemeh ramezani wrote: Dear all After simulation of gold-protein interaction, now I want to calculate binding energy of each residue to gold. but when I use g_energy command appear this error: No distance restraints in topology How can I calculate binding energy without running simulation again(because it takes about one week and I need this result as soon as possible) ? Please provide the exact command you used. There is no reason for g_energy to be reading a topology to extract this information. You can get so-called nonbonded interaction energies decomposed by energy group, but whether or not you can call this an actual binding energy is highly questionable. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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] binding energy calculation when appear this error: no distance restraints in topology
On 4/14/13 3:09 PM, fatemeh ramezani wrote: the command that I used is : g_energy-f md300.edr -s fws_md300.tpr-o energy.xvg-pairs pairs.xvg The -pairs option is not relevant for what you are trying to do. From g_energy -h: Additionally running time-averaged and instantaneous distances between selected pairs can be plotted with the -pairs option. This option is only to be used when employing distance restraints, hence g_energy fails when it finds none. You need neither -pairs nor -s. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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] g_hbond : autocorrelation funciton
Hello, I am calculating the hyrogen bond life time my system using g_hbond in Gromacs. Program calculate the hydrogen bond life time from the autocorrelation function. Program calculate the hydrogen bond autocorrelation function with the hydrogen bond criteria. What quantity program use such as distance between donor-acceptor, to calculate the autocorrelation function? Thanks Nilesh -- 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] g_hbond : autocorrelation funciton
On 4/14/13 7:21 PM, Nilesh Dhumal wrote: Hello, I am calculating the hyrogen bond life time my system using g_hbond in Gromacs. Program calculate the hydrogen bond life time from the autocorrelation function. Program calculate the hydrogen bond autocorrelation function with the hydrogen bond criteria. What quantity program use such as distance between donor-acceptor, to calculate the autocorrelation function? This is an adjustable option. Please read g_hbond -h. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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] g_hbond : autocorrelation funciton
-ac: average over all autocorrelations of the existence functions (either 0 or 1) of all hydrogen bonds. Program collect the data 0 or 1 along time? nilesh On 4/14/13 7:21 PM, Nilesh Dhumal wrote: Hello, I am calculating the hyrogen bond life time my system using g_hbond in Gromacs. Program calculate the hydrogen bond life time from the autocorrelation function. Program calculate the hydrogen bond autocorrelation function with the hydrogen bond criteria. What quantity program use such as distance between donor-acceptor, to calculate the autocorrelation function? This is an adjustable option. Please read g_hbond -h. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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] g_hbond : autocorrelation funciton
On 4/14/13 8:00 PM, Nilesh Dhumal wrote: -ac: average over all autocorrelations of the existence functions (either 0 or 1) of all hydrogen bonds. Program collect the data 0 or 1 along time? The presence of a hydrogen bond is a binary function. Either it exists (1) or does not (0). Whether or not a hydrogen bond exists depends on distance and angle criteria. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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] pbc problem
Thank Justin ! I used the command editconf -center and i saw my membrane was in center of the box. I am stupid in that how putting the bilayer in a periodic image (instead between two periodic images as it was). Can you give me some instructions ? Many thanks ! On Fri, Apr 12, 2013 at 6:52 PM, Justin Lemkul jalem...@vt.edu wrote: On Fri, Apr 12, 2013 at 7:48 AM, Kieu Thu Nguyen kieuthu2...@gmail.com wrote: Dear All, I made a POPC bilayer and carried out embedding a protein into this membrane. But the fatal error has appeared : Fatal error: Something is wrong with your membrane. Max and min z values are 12.342000 and 0.016000. Maybe your membrane is not centered in the box, but located at the box edge in the z-direction, so that one membrane is distributed over two periodic box images. Another possibility is that your water layer is not thick enough. I think my bilayer stay at between two periodic images. What should i do to put it in corrected position ? It should be a very simple matter of visualization. Use editconf -center to place the membrane wherever you want within the unit cell. You can remove the uncertainty (I think is weak compared to I know) by looking at the box vectors and then numerically determining the center of the membrane with g_traj. That should provide you with all the information you need to determine what's going on. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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] Issue with domain decomposition between v4.5.5 and 4.6.1
Dear all, I am running a NPT simulation of 33,534 tip4P waters, and I am using domain decomposition as the parallelization scheme. Previously, I had been using Gromacs version 4.5.5 but have recently installed and switched to Gromacs version 4.6.1. Using Gromacs 4.5.5 I can successfully run my water box using domain decomposition over many different processor numbers. However the same simulation returns the following error when I try Gromacs 4.6.1 The initial number of communication pulses is: X 1 Y 1 Z 1 The initial domain decomposition cell size is: X 2.48 nm Y 2.48 nm Z 1.46 nm When dynamic load balancing gets turned on, these settings will change to: The maximum number of communication pulses is: X 1 Y 1 Z 1 The minimum size for domain decomposition cells is 1.000 nm The requested allowed shrink of DD cells (option -dds) is: 0.80 The allowed shrink of domain decomposition cells is: X 0.40 Y 0.40 Z 0.68 The above error occurred running over 16 nodes / 128 processors. The system runs for version 4.6.1 for 1,8, and 16 processors but not for 32,64, or 128 processors. I have tried other systems (including NVT, Berendsen/PR barostats, anisotropic/isotropic ) at the higher number of processors using both version 4.5.5 and 4.6.1 and get the same result - v4.5.5 runs fine while v4.6.1 returns the error type listed above. Is anyone else having a similar issue? Is there something I am not considering? Any help would be greatly appreciated! The details I have used to compile each code are below. My log files indicate that I am indeed calling the correct executable at run time. Thanks in advance! Stephanie --- Computer architecture: SUN X6275 blades CPU: 2.93 GHz dual socket/quad core, Nehalem X5570 processors Version 4.5.5 Compiler: openmpi-1.4.3_oobpr_intel-11.1-f064-c064 / intel-11.1-f064-c064 ./configure COMPILER=intel-11.1-f064-c064 CC=mpicc CXX=mpicpc CLINKER=mpicc FC=mpif90 F77=mpif77 --without-x --disable-threads --enable-mpi --enable-shared --prefix=mypath --oldincludedir=mypath Version 4.6.1 Complier: openmpi-1.4.3_oobpr_intel-12.1-2011.7.256 / intel-12.1-2011.7.256 CC=mpicc CXX=mpicxx FC=mpif90 F77=mpif77 cmake -DGMX_CPU_ACCELERATION=SSE2 -DGMX_PREFER_STATIC_LIBS=ON -DBUILD_SHARED_LIBS=OFF -DGMX_BUILD_OWN_FFTW=ON -DCMAKE_INSTALL_PREFIX=mypath -DGMX_DEFAULT_SUFFIX=ON -DGMX_MPI=ON -- 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] specbond detection
Dear gmx, I have mentioned the minimum distance FE bonds to C, O and NE2 (from HIS) in specbond file. As per specbond, the pdb2gmx detect these all bonds and shown in topology file. However, except the FE-C and FE-NE2, i couldn't able to visualize the bonds of FE-O and the bonds between the FE to their pyrrole nitrogen. I looked over the ffbonded.itp file and it looks fine with proper bond angle dihdedral details. What i am missing here? Advance thanks for your comments. Raju -- 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
