Re: [gmx-users] ligand moving out during umbrella sampling
On Thu, May 11, 2017 at 9:03 PM, Justin Lemkul wrote: > > > On 5/11/17 9:21 AM, abhisek Mondal wrote: > >> On Thu, May 11, 2017 at 11:02 AM, abhisek Mondal >> wrote: >> >> Hi, >>> >>> Thank you for the explanation. It really cleared some concepts. But I'm >>> still having my ligand moving in this step. I have modified the code as: >>> ; Pull code >>> pull= umbrella >>> pull_ngroups= 1 >>> pull_group0 = Protein_chain_A >>> pull_group1 = ACO >>> pull_geometry = direction ; simple distance increase >>> pull_dim = Y Y Y ; not to allow ligand move along other >>> dir >>> pull_rate1 = 0.0 >>> pull_k1 = 1000 ; kJ mol^-1 nm^-2 >>> pull_start = yes ; define initial COM distance > 0 >>> pull_vec1 = 0 0 -1 >>> >>> > Note that with "direction" geometry, only pull_vec1 is acting. pull_dim > is ignored. > > The ligand was previously moving along x,y direction when I was using >>> pull_dim = N N Y. So I changed it to Y in all direction and provided 0 >>> as >>> vector and pull_rate1=0.0, so that it does not move much. But at the end >>> of a 10ns run, I see that the ligand is still moving as it was earlier. >>> >>> It shows me: >> Pull group natoms pbc atom distance at start reference at t=0 >>0 1132936665 >>159 1618 -1.555-1.555 >> Is it ok withe negative value ? Anyway this setup is not working. >> >> > Again you're trying to just apply the restraint to one dimension and it > looks to be fairly arbitrary. I already suggested using the vector > connecting the ligand COM with the binding site residues' COM and using > that as pull_vec1. Draw it out. It makes a lot more sense than trying to > restrain only along one axis, which as I have said before, makes no sense > in this case. > > Thank you for such detailed suggestion. I followed on as per your suggestion. Calculated COM of protein and Ligand. Calculated protein-lig vector (using COM) to be used for pulling (as pull_vec1). Pulling also achieved successfully. But after pulling, when I performed the brief npt_umbrella run with pull_rate1=0, I found the ligand is moving little bit. Could not understand what I have mistaken this time. So I moved on for umbrella sampling mdrun step, with pull_rate1=0 and pull_vec1=as determined from COM calculations. Despite I found that the ligand is moving vigorously and got pulled away probably. I'm putting npt_umbrella.mdp,md_umbrella.mdp,conf140.gro(used for npt_umbrella), npt140.gro,md_umbrella run video in the following link: https://drive.google.com/drive/folders/0B6O-L5Y7BiGJQ1FIc2tIRFE2dE0 Am I still missing some drastic steps ? Please suggest me if I do. I'm totally lost here in this regard. > -Justin > > >>> I have choose my reaction coordinate to be along -Z axis and want to >>> apply >>> biasing potential accordingly with restraining the ligand movement. Can >>> you >>> please suggest where am I failing with this code ? >>> >>> Thank you. >>> >>> >>> >>> On Tue, May 9, 2017 at 1:11 AM, Justin Lemkul wrote: >>> >>> On 5/8/17 10:00 AM, abhisek Mondal wrote: On Sun, May 7, 2017 at 11:37 PM, Justin Lemkul wrote: > > > >> On 5/7/17 1:57 AM, abhisek Mondal wrote: >> >> Hi, >> >>> >>> For your ease of understanding regarding what is happening during >>> this >>> above said umbrella-mdrun, I have shared the trajectory video file >>> the >>> following link. >>> https://drive.google.com/drive/folders/0B6O-L5Y7BiGJQ1FIc2tIRFE2dE0 >>> >>> Is this normal given that the mdp code being used ? I basically have >>> no >>> idea with this step, so please help me out. I'm using gromacs-4.6.2. >>> >>> >>> Your setup is incorrect. You're applying a biasing potential only >>> >> along >> z, so the ligand can move freely along x and y. A protein-ligand >> complex >> has spherical symmetry, so you should set the reaction coordinate to >> the >> vector connecting the ligand with some suitable subset of interacting >> protein residues. >> >> > > I don't get it. > We are trying not to move our configuration (generated after pulling > simulation) along the reaction coordinate, so for restraining we are > supposed to set pull_rate1=0.0. > > Of course. But you said set pull_k = 0 which does not make sense. The pulling rate *is* zero during umbrella sampling (no net displacement, restrain to the specified distance along the reaction coordinate) and pulling force constant should be non-zero. If applying biasing potential only along z is causing movement along x and > y then what if we apply the biasing potential along x,y,z ? Will it > cause > any good in restraining the ligand? > > > This is how it sho
Re: [gmx-users] Anyone use FMA (Functional Mode Analysis) ?
Thank you. I have just received the response from Dr. Jochen Hub and solved this problem.Qing At 2017-05-14 22:42:30, "Qing Lv" wrote: >Hi Colleagues, > >I am trying to compile FMA (Functional Mode Analysis), developed by Dr. Jochen >Hub. However, I met difficulties in the installation. According to the >instructions, I installed Gromacs 4.0.5 (also tried 4.0.7) and the related >libraries (libf2c, lapack, mpich, etc). >Firstly, cmake . did not give error messages; >When executing make, I got the following messages: >[ 80%] Building C object >CMakeFiles/fma.dir/files/gromacs-4.0.5/src/tools/eigensolver.c.o >/files/gromacs-4.0.5/src/tools/eigensolver.c: In function ‘eigensolver’: >/files/gromacs-4.0.5/src/tools/eigensolver.c:65: warning: unused variable ‘iu’ >/files/gromacs-4.0.5/src/tools/eigensolver.c:65: warning: unused variable ‘il’ >Linking C executable fma >/usr/bin/ld: cannot find -lmd_mpi >collect2: ld returned 1 exit status >make[2]: *** [fma] Error 1 >make[1]: *** [CMakeFiles/fma.dir/all] Error 2 >make: *** [all] Error 2 > > >I googled this message but have not found useful info. Also, it seems that Dr. >Hub might have stopped the maintenance of this program. >It seems that "-lmd_mpi" is a component of Gromacs. I tried higher GMX >versions like 4.5.4, but found it incompatible with FMA. Have anyone used this >program? Any help is highly appreciated. > > >Thanks a lot. >Qing >-- >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] Anyone use FMA (Functional Mode Analysis) ?
Hi Colleagues, I am trying to compile FMA (Functional Mode Analysis), developed by Dr. Jochen Hub. However, I met difficulties in the installation. According to the instructions, I installed Gromacs 4.0.5 (also tried 4.0.7) and the related libraries (libf2c, lapack, mpich, etc). Firstly, cmake . did not give error messages; When executing make, I got the following messages: [ 80%] Building C object CMakeFiles/fma.dir/files/gromacs-4.0.5/src/tools/eigensolver.c.o /files/gromacs-4.0.5/src/tools/eigensolver.c: In function ‘eigensolver’: /files/gromacs-4.0.5/src/tools/eigensolver.c:65: warning: unused variable ‘iu’ /files/gromacs-4.0.5/src/tools/eigensolver.c:65: warning: unused variable ‘il’ Linking C executable fma /usr/bin/ld: cannot find -lmd_mpi collect2: ld returned 1 exit status make[2]: *** [fma] Error 1 make[1]: *** [CMakeFiles/fma.dir/all] Error 2 make: *** [all] Error 2 I googled this message but have not found useful info. Also, it seems that Dr. Hub might have stopped the maintenance of this program. It seems that "-lmd_mpi" is a component of Gromacs. I tried higher GMX versions like 4.5.4, but found it incompatible with FMA. Have anyone used this program? Any help is highly appreciated. Thanks a lot. Qing -- 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] Graphene modeling
Hi GROMACS users, I want to model a graphene sheet. I used the instruction stated in link http://www.gromacs.org/Documentation/How-tos/Carbon_Nanotube. I put the cnt_oplsaa.ff folder in the directory where I want to run the rest of the work. Also, I rename the residues of the graphene to “CJ” and the atoms to “C”. but, when I want to use “gmx x2top”, I get the error that says it cannot find any forcefield type for the atoms. Can you please help me to figure this out? Best, Mohammad -- 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] ligand moving out during umbrella sampling
On Thu, May 11, 2017 at 9:03 PM, Justin Lemkul wrote: > > > On 5/11/17 9:21 AM, abhisek Mondal wrote: > >> On Thu, May 11, 2017 at 11:02 AM, abhisek Mondal >> wrote: >> >> Hi, >>> >>> Thank you for the explanation. It really cleared some concepts. But I'm >>> still having my ligand moving in this step. I have modified the code as: >>> ; Pull code >>> pull= umbrella >>> pull_ngroups= 1 >>> pull_group0 = Protein_chain_A >>> pull_group1 = ACO >>> pull_geometry = direction ; simple distance increase >>> pull_dim = Y Y Y ; not to allow ligand move along other >>> dir >>> pull_rate1 = 0.0 >>> pull_k1 = 1000 ; kJ mol^-1 nm^-2 >>> pull_start = yes ; define initial COM distance > 0 >>> pull_vec1 = 0 0 -1 >>> >>> > Note that with "direction" geometry, only pull_vec1 is acting. pull_dim > is ignored. > > The ligand was previously moving along x,y direction when I was using >>> pull_dim = N N Y. So I changed it to Y in all direction and provided 0 >>> as >>> vector and pull_rate1=0.0, so that it does not move much. But at the end >>> of a 10ns run, I see that the ligand is still moving as it was earlier. >>> >>> It shows me: >> Pull group natoms pbc atom distance at start reference at t=0 >>0 1132936665 >>159 1618 -1.555-1.555 >> Is it ok withe negative value ? Anyway this setup is not working. >> >> > Again you're trying to just apply the restraint to one dimension and it > looks to be fairly arbitrary. I already suggested using the vector > connecting the ligand COM with the binding site residues' COM and using > that as pull_vec1. Draw it out. It makes a lot more sense than trying to > restrain only along one axis, which as I have said before, makes no sense > in this case. As to obtain COM of ligand I'm using: "g_traj_mpi -ox aco_com -com -s npt.tpr" and taking the last frame's xy,z coordinate from the .xvg file generated from that command. 394 14.1362 14.4649 5.94131 395 14.1435 14.45 5.94041 396 14.0858 14.4461 5.90442 397 14.1398 14.4164 5.86902 398 14.1514 14.4434 5.8461 399 14.1344 14.421 5.88976 400 14.1996 14.4613 5.82814 Is this approach correct for taking COM? Another question is that, how can I calculate COM for specific set of residues ? If the above approach (for calculating Ligand COM) is correct then it allows calculation of COM for whole protein only. Please do suggest a way. Thank you. > > -Justin > > >>> -- 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.
