Re: [gmx-users] Autocorrelation times from gmx wham and analyze
Den 2018-09-05 kl. 13:01, skrev Gmx QA: Hi all, I am running a series of umbrella sampling simulations of a drug across a membrane, with the final aim to determine permeability using the local diffusion model. I have come across papers where the (necessary) autocorrelation times of the mean-squared fluctuation of the coordinates are calculated using gmx wham, and this is also what I have done like this: gmx wham -if pullf-files.dat -it tpr-files.dat -o -hist -ac -oiact and then the ac-times are written to the file iact.xvg. To understand better the procedure however, I also wanted to do a similar calculation manually. I therefore did this: gmx traj -f ../umbrella0.part0001.xtc -s ../umbrella0.tpr -ox umbrella0_z_com.xvg -com -nox -noy to extract the z-com-coordinates of the drug molecule for a particular us window. Then: gmx analyze -f umbrella0_z_com.xvg -ac -fitfn exp Followed by: gmx analyze -f autocorr.xvg -integrate to get what I though was going to be the equivalent acf-time tau. However, for this umbrella window gmx wham gives me tau = 2.25 whereas the second approach gives a value of 122. What could be the reason for this difference? There is some info in cmx wham that says that the act calculation is cut at a value of 0.05, and that is something that I haven't been able to replicate in my second approach, but any insights are highly appreciated. Technical question first. Are you storing the xtc file with the same frequency as the data in the pullx or pullf files? Cheers /PK -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.uu.se -- 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] i have a question about multiple chain simulation at the same box
On 9/5/18 9:25 AM, milad bagheri wrote: I'm going to examine the interaction between the two proteins using molecular dynamics simulation by gromacs, so I downloaded pdb code 5op1 from the rcsb , which has two protein(Complex). I want to create a gap between two protein, and then with the same coordinate Put these two proteins in a box and run MD 100 nanoseconds, for validation this trick compare rmsd x-ray pose and Md pose. please help me ... Separate the coordinates of the two proteins, translate one of them with editconf, and concatenate the new coordinates back together. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Justin paper 2010 pulling
On 9/5/18 1:50 AM, Rakesh Mishra wrote: So that means It is may be due to the difference in the type of interaction. and I can not understand your this statement "you have to contend with forces principally acting perpendicular to the direction of the bias" Well, what interactions act along the plane perpendicular to the helix axis of a duplex DNA or RNA? -Justin On Tue, Sep 4, 2018 at 10:54 PM, Justin Lemkul wrote: On 9/4/18 11:44 AM, Rakesh Mishra wrote: Dear Justin, Seriously I want to remove my confusion. I just read your one paper " J.Physical Chemistry B 2010, 114, 1652-60" Where you have studied stability of Alzheimer. I don't want to ask about umbrella sampling used for the calculation of PMF. But , before the calculation of PMF , you have obtained simple dissociation using your pulling protocol of gromacs with constant velocity simulation at three different velocities. I am surprised that you have followed the obvious protocol of minimization the nvt the npt and then 100ns md production. then you took final structure of 100ns and made new box for pulling and followed the same minimisation and npt for short time. After this you did pulling along only one direction (one reaction coordinate) . I am surprised that how such a smooth force/time data you have obtained for all the velocities (0.01,0.001,0.005) . I am asking because for my simple 12bp dsDNA or 22bp siRNA , I also have followed similar protocol and fixed one end (say 5') of first strand and pulling opposite end (5') of second strand along the helical direction of the system. Here, I am getting force/time (in the .xvg ) data which is qualitatively similar behaviour like yours i.e. initially increasing then reach to maximum and then decreasing almost becomes to zero value. But , In mine case during initial time of pulling force is also negative as well large fluctuation of force . But not such a smooth Variation of force/time like your in this paper. In your case, force is increasing like linearly in the initial and reaches the maximum and then start to decrease. There is no problem to clarify the peak of force (maximum force) in your pulling (above mentioned paper). While in our case its very difficult to clarify the peak force due to large fluctuation in value. Can you please tell me something about the reason. Its smoothness is now became headache for my calculation in all the case of pulling. There is no reason to think that your outcome and mine should look anything alike. Pulling apart two proteins that interact in the way the peptides do in a protofibril is much simpler than the intertwined nature of a DNA or RNA duplex. If you pull along the helix axis, you have to contend with forces principally acting perpendicular to the direction of the bias, as well as the fact that the strands have to slide past one another, requiring major distortion of the helix and/or frictional forces due to the individual strands unwinding from one another. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support /Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Orthorhombic structure and Lincs warnings
It's not the first time you're posting this message and there's a reason noone is replying. 1. What are the inter-axis angles of that orthorhombic box? Why not a rectangular box? 2. Why are you using LINCS with graphene, which should _not_ be simulated with constraints? 3. Why are you restraining your system on top of everything else? 4. Did you verify that your graphene model (without constraints or restraints) was stable prior to adding water? Alex On Wed, Sep 5, 2018 at 1:35 PM sagar bathla wrote: > Dear all, > > Can simulation for orthorhombic structure be done in gromacs? > Actually I am working with 2-D graphene sheets which are like a > parallelogram. > > In my system, there is a graphene sheet (restrained)and water. > After the energy minimization, energy is coming positive (order of 10^8) > On Visualization in vmd, the structure appears to be rectangle and there > comes a warning with it > > 152 inconsistant shifts etc. > > When I am trying to equillibrate the system then so many lines warnings > appears of rotation of bonds more than 90 degrees and simulation crashes > everytime. > > Is there any problem with structure or y else? > Earlier also I posted this but issue hasn't resolved yet. > > Please help me to find this problem. > > Regards > Sagar > -- > 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] Orthorhombic structure and Lincs warnings
Dear all, Can simulation for orthorhombic structure be done in gromacs? Actually I am working with 2-D graphene sheets which are like a parallelogram. In my system, there is a graphene sheet (restrained)and water. After the energy minimization, energy is coming positive (order of 10^8) On Visualization in vmd, the structure appears to be rectangle and there comes a warning with it 152 inconsistant shifts etc. When I am trying to equillibrate the system then so many lines warnings appears of rotation of bonds more than 90 degrees and simulation crashes everytime. Is there any problem with structure or y else? Earlier also I posted this but issue hasn't resolved yet. Please help me to find this problem. Regards Sagar -- 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] Pressure control with constraints incompatible with expanded ensemble
Hi all, I would like to use Gromacs (2018 versions on GPUs) to compute solvation free energies using expanded ensemble simulations. I have no problems in the NVT ensemble, but when I try and implement pressure control I run into errors. Specifically, if I want to use expanded ensemble, I must use the md-vv integrator. If I use this integrator, I must select MTTK pressure control (I’d rather not use Berendsen for production runs), but if I want to constrain hydrogen bonds, I cannot use MTTK (grompp throws an error). Previous versions of Gromacs appear to have allowed MTTK as long as SHAKE was used for constraints (see the mdp files here: http://www.alchemistry.org/wiki/GROMACS_4.6_example:_Ethanol_solvation_with_expanded_ensemble). So is the only way to run NPT, expanded ensemble simulations with current versions of Gromacs to use the Berendsen barostat? Thanks, Jacob -- 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] compilation terminated with error
Dear all, The compilation of the Gromacs.2018.2 on a cluster terminated with error in below step, would you please let me know how I can overcome the issue? I use gcc/7.3.0. [ 0%] Building C object src/gromacs/CMakeFiles/tng_io_zlib.dir/__/external/tng_io/external/zlib/crc32.c.o cd /p/home/alex/.local/gromacs/2018.2/gromacs-2018.2/build/src/gromacs && /opt/cray/pe/craype/2.5.13/bin/cc -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -isystem /p/home/alex/.local/gromacs/2018.2/gromac s-2018.2/src/external/lmfit -I/p/home/alex/.local/gromacs/2018.2/gromacs-2018.2/build/src -isystem /p/home/alex/.local/gromacs/2018.2/gromacs-2018.2/src/external/thread_mpi/include -I/p/hom e/alex/.local/gromacs/2018.2/gromacs-2018.2/src -isystem /usr/include -isystem /opt/cray/pe/fftw/3.3.4.11/broadwell/include -I/p/home/alex/.local/gromacs/2018.2/gromacs-2018.2/src/external/ tng_io/external/zlib -msse2 -dynamic -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/tng_io_zlib.dir/__/external/tng_io/external/zlib/crc32.c.o -c /p/h ome/alex/.local/gromacs/2018.2/gromacs-2018.2/src/external/tng_io/external/zlib/crc32.c make[2]: Leaving directory '/p/home/alex/.local/gromacs/2018.2/gromacs-2018.2/build' make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/build make[2]: Entering directory '/p/home/alex/.local/gromacs/2018.2/gromacs-2018.2/build' make[2]: Entering directory '/p/home/alex/.local/gromacs/2018.2/gromacs-2018.2/build' make[2]: Entering directory '/p/home/alex/.local/gromacs/2018.2/gromacs-2018.2/build' In file included from /opt/gcc/7.3.0/snos/include/g++/ext/string_conversions.h:41:0, from /opt/gcc/7.3.0/snos/include/g++/bits/basic_string.h:6349, from /opt/gcc/7.3.0/snos/include/g++/string:52, from /p/home/alex/.local/gromacs/2018.2/gromacs-2018.2/src/programs/view/view.cpp:45: /opt/gcc/7.3.0/snos/include/g++/cstdlib:75:15: fatal error: stdlib.h: No such file or directory #include_next ^~ compilation terminated. Thank you. Regards, 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] Workstation choice
Hi Olga, The authors of: https://github.com/bio-phys/MDBenchmark/tree/version-1.3.2 https://zenodo.org/record/1318123 May be helpful. If your data is not confidential, you may consider running Gromacs remotely on a cloud high performance computing resource, or benchmarking remotely and then purchasing a suitable configuration. Some other information: http://manual.gromacs.org/documentation/current/user-guide/mdrun-performance.html# http://www.gromacs.org/GPU_acceleration https://extras.csc.fi/chem/courses/gmx2007/Erik_Talks/building_clusters.pdf http://www.gromacs.org/Documentation/Performance_checklist On 09/05/2018 12:02 PM, Olga Selyutina wrote: Hello, I need help in choice of the workstation for MD simulations using GROMACS. It is supposed to study systems consisting from 30-50k atoms, in particular, lipid bilayer models. Since the last generation of Intel and Ryzen CPU has made a big leap in performance, available workstation can’t be taken as a basis. Please, help to choose components of the workstation, particularly, GPU and CPU with total cost about $2000. What is better, to buy two GPUs(sli) or one GPU but more effective? -- 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] Calculating the Hydrophobic and Hydrophilic SASA values on GROMACS version 5.1.2
Hi Supid, Got the point. Thanks a lot. On Wed, Sep 5, 2018 at 2:05 AM, Sudip Das wrote: > Hi Andrew, > Follow the below link. Hope that helps. > > http://www.gromacs.org/Documentation/How-tos/Tool_Changes_for_5.0 (follow > the 'g_sas' section) > > Regards, > Sudip > > On Wed, Sep 5, 2018 at 9:56 AM Andrew Srimalka Wijesekera < > 2014s14...@stu.cmb.ac.lk> wrote: > > > Dear all, > > > > I'm currently studying the structural changes and thermodynamic > properties > > of a protein structure when binding the ligand. Here I have ran the MD > run > > for 50 ns and calculate the SASA value from the gromacs 5.1.2 version. > > According to my knowledge I got only the total SASA value. But I want to > > get the hydrophobic and hydrophilic SASA values seperately from the > gromacs > > 5.1.2 version as well. Therefore would you please help me to solve this > > problem. > > Thanks in advance. > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > > -- > 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] i have a question about multiple chain simulation at the same box
I'm going to examine the interaction between the two proteins using molecular dynamics simulation by gromacs, so I downloaded pdb code 5op1 from the rcsb , which has two protein(Complex). I want to create a gap between two protein, and then with the same coordinate Put these two proteins in a box and run MD 100 nanoseconds, for validation this trick compare rmsd x-ray pose and Md pose. please help me ... -- 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] Autocorrelation times from gmx wham and analyze
Hi all, I am running a series of umbrella sampling simulations of a drug across a membrane, with the final aim to determine permeability using the local diffusion model. I have come across papers where the (necessary) autocorrelation times of the mean-squared fluctuation of the coordinates are calculated using gmx wham, and this is also what I have done like this: gmx wham -if pullf-files.dat -it tpr-files.dat -o -hist -ac -oiact and then the ac-times are written to the file iact.xvg. To understand better the procedure however, I also wanted to do a similar calculation manually. I therefore did this: gmx traj -f ../umbrella0.part0001.xtc -s ../umbrella0.tpr -ox umbrella0_z_com.xvg -com -nox -noy to extract the z-com-coordinates of the drug molecule for a particular us window. Then: gmx analyze -f umbrella0_z_com.xvg -ac -fitfn exp Followed by: gmx analyze -f autocorr.xvg -integrate to get what I though was going to be the equivalent acf-time tau. However, for this umbrella window gmx wham gives me tau = 2.25 whereas the second approach gives a value of 122. What could be the reason for this difference? There is some info in cmx wham that says that the act calculation is cut at a value of 0.05, and that is something that I haven't been able to replicate in my second approach, but any insights are highly appreciated. Cheers /PK -- 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] Calculating the Hydrophobic and Hydrophilic SASA values on GROMACS version 5.1.2
Hi Andrew, Follow the below link. Hope that helps. http://www.gromacs.org/Documentation/How-tos/Tool_Changes_for_5.0 (follow the 'g_sas' section) Regards, Sudip On Wed, Sep 5, 2018 at 9:56 AM Andrew Srimalka Wijesekera < 2014s14...@stu.cmb.ac.lk> wrote: > Dear all, > > I'm currently studying the structural changes and thermodynamic properties > of a protein structure when binding the ligand. Here I have ran the MD run > for 50 ns and calculate the SASA value from the gromacs 5.1.2 version. > According to my knowledge I got only the total SASA value. But I want to > get the hydrophobic and hydrophilic SASA values seperately from the gromacs > 5.1.2 version as well. Therefore would you please help me to solve this > problem. > Thanks in advance. > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- 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] Workstation choice
Hello, I need help in choice of the workstation for MD simulations using GROMACS. It is supposed to study systems consisting from 30-50k atoms, in particular, lipid bilayer models. Since the last generation of Intel and Ryzen CPU has made a big leap in performance, available workstation can’t be taken as a basis. Please, help to choose components of the workstation, particularly, GPU and CPU with total cost about $2000. What is better, to buy two GPUs(sli) or one GPU but more effective? -- Best rerards, Olga Selyutina -- 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.
