[gmx-users] gmx bar
Hi gromacs users, I'm using gmx bar to plot my free energy calculation results with the command: gmx bar *xvg -o -oh -oi I obtain the graphic bar.xvg where DG are reported on Y axis and the number of lambda steps (0,1,2,3...) on the X. I'd like to get a graphic where the values of my lambdas (0.05, 0,10, 0,15,...,1) are reported on X axis instead. Is it possible? Best regards, Davide Bonanni -- Davide Bonanni, PhD student Dept. Science and Drug Technology University of Turin (UniTO) - Italy Mobile +39 3409726272 <+39%20340%20972%206272> -- -- 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] Crash in minimization that involves dummy atoms
Hi gromacs users, I'm doing a relative free energy calculation of a ligand-protein complex. I'm transforming a hydrogen atom into methyl. I have generated input topology with FESetup. When I try to run minimization I get that error: """ Energy minimization has stopped, but the forces have not converged to the Requested precision Fmax It stopped because the algorithm tried to make a new step whose size was too Small, or there was no change in the energy since last step. Either way, we Regard the minimization as converged to within the available machine Precision, given your starting configuration and EM parameters. Double precision normally gives you more accuracy, but this is often not Needed for preparing to run molecular dynamics. You may need to increase your constraint accuracy, or turn Off constraints altogether (set constraints = none in mdp file) Steepest Descents converged to machine precision in 50 steps, But did not reach the requested Fmax <100. Potential Energy = 1.1698845e + 07 Maximum force = 7.4549694e + 05 is atom 5745 Norm of force = 3.5688174e + 03 """ As you can see the Potential Energy is too high and if a look at the system I got is completely messed up. Exactly the same complex with the same parameters but a different perturbation (H -> Cl) gave me no problems. So the minimization crash should be related to the presence of dummy atoms. I read some discussion about the same topic but I was not able to find a solution. Everything looks good to me, I do not see anything wrong in the file .gro or .top. I have tried also to run the same minimization on T4 lysozyme tutorial input (https://ccpforge.cse.rl.ac.uk/gf/project/ccpbiosim/wiki/? pagename=T4+lysozyme), and when there are dummy atom involved I obtain the same problem. Probably I'm missing something in the .mdp or there is some error I can not see. I tried to modify constraint but nothing changed. Any kind of suggestion is really appreciated, thank you in advance. Cheers, Davide Bonanni This is the first part of ligand's topology: """ [ moleculetype ] LIG 3 [ atoms ] ; nr type resno resnm atomcgnr chargemass typeB chargeB massB 1 c1 LIG C1 10.667751 12.0100 c 0.667700 12.0100 2 cc 1 LIG C2 2 -0.469349 12.0100 cc -0.471400 12.0100 3 ca 1 LIG C3 30.034751 12.0100 ca 0.039700 12.0100 4 ca 1 LIG C4 4 -0.083249 12.0100 ca -0.032600 12.0100 5 c1 LIG C5 50.742351 12.0100 c 0.742300 12.0100 6 ca 1 LIG C6 60.121651 12.0100 ca 0.122600 12.0100 7 ca 1 LIG C7 70.029951 12.0100 ca 0.029400 12.0100 8 ca 1 LIG C8 80.029951 12.0100 ca 0.029400 12.0100 9 ca 1 LIG C9 90.134451 12.0100 ca 0.134400 12.0100 10 ca 1 LIG C10 100.134451 12.0100 ca 0.134400 12.0100 11 cp 1 LIG C11 11 -0.137949 12.0100 cp -0.139000 12.0100 12 cp 1 LIG C12 12 -0.012949 12.0100 cp -0.013000 12.0100 13 ca 1 LIG C13 13 -0.108449 12.0100 ca -0.109000 12.0100 14 ca 1 LIG C14 14 -0.108449 12.0100 ca -0.109000 12.0100 15 ca 1 LIG C15 15 -0.136949 12.0100 ca -0.137000 12.0100 16 ca 1 LIG C16 16 -0.136949 12.0100 ca -0.137000 12.0100 17 ca 1 LIG C17 17 -0.134949 12.0100 ca -0.135000 12.0100 18 ca 1 LIG C18 18 -0.155949 12.0100 ca -0.158000 12.0100 19 ca 1 LIG C19 19 -0.122949 12.0100 ca -0.122000 12.0100 20 ca 1 LIG C20 20 -0.226949 12.0100 ca -0.223000 12.0100 21 f1 LIG F21 21 -0.109349 19. f -0.109400 19. 22 f1 LIG F22 22 -0.130849 19. f -0.131400 19. 23 f1 LIG F23 23 -0.130849 19. f -0.131400 19. 24 f1 LIG F24 24 -0.109349 19. f -0.109400 19. 25 nc 1 LIG N25 25 -0.632449 14.0100 nc -0.632500 14.0100 26 na 1 LIG N26 260.281751 14.0100 na 0.281700 14.0100 27 n 1 LIG N27 27 -0.465049 14.0100 n -0.464100 14.0100 28 o 1 LIG O28 28 -0.704049 16. o -0.705100 16. 29 o 1 LIG O29 29 -0.651049 16. o -0.652100 16. 30 h4 1 LIG H30 300.158051 1.0080 c3 -0.035800 12.0100 31 ha 1 LIG H31 310.141051 1.0080 ha 0.141000 1.0080 32 ha
[gmx-users] Help on MD performance, GPU has less load than CPU.
Hi, I am working on a node with Intel(R) Xeon(R) CPU E5-2630 v3 @ 2.40GHz, 16 physical core, 32 logical core and 1 GPU NVIDIA GeForce GTX 980 Ti. I am launching a series of 2 ns molecolar dynamics simulations of a system of 6 atoms. I tried diverse setting combination, but however i obtained the best performance with the command: "gmx mdrun -deffnm md_LIG -cpt 1 -cpo restart1.cpt -pin on" which use 32 OpenMP threads, 1 MPI thread, and the GPU. At the end of the file.log of molecular dynamic production I obtain this message: "NOTE: The GPU has >25% less load than the CPU. This imbalance causes performance loss." I don't know how can improve the load on CPU more than this, or how I can decrease the load on GPU. Do you have any suggestions? Thank you in advance. Cheers, Davide Bonanni Initial and final part of LOG file here: Log file opened on Sun Jul 9 04:02:44 2017 Host: bigblue pid: 16777 rank ID: 0 number of ranks: 1 :-) GROMACS - gmx mdrun, VERSION 5.1.4 (-: GROMACS: gmx mdrun, VERSION 5.1.4 Executable: /usr/bin/gmx Data prefix: /usr/local/gromacs Command line: gmx mdrun -deffnm md_fluo_7 -cpt 1 -cpo restart1.cpt -pin on GROMACS version:VERSION 5.1.4 Precision: single Memory model: 64 bit MPI library:thread_mpi OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 32) GPU support:enabled OpenCL support: disabled invsqrt routine:gmx_software_invsqrt(x) SIMD instructions: AVX2_256 FFT library:fftw-3.3.4-sse2-avx RDTSCP usage: enabled C++11 compilation: disabled TNG support:enabled Tracing support:disabled Built on: Tue 8 Nov 12:26:14 CET 2016 Built by: root@bigblue [CMAKE] Build OS/arch: Linux 3.10.0-327.el7.x86_64 x86_64 Build CPU vendor: GenuineIntel Build CPU brand:Intel(R) Xeon(R) CPU E5-2630 v3 @ 2.40GHz Build CPU family: 6 Model: 63 Stepping: 2 Build CPU features: aes apic avx avx2 clfsh cmov cx8 cx16 f16c fma htt lahf_lm mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdrnd rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic C compiler: /bin/cc GNU 4.8.5 C compiler flags:-march=core-avx2-Wextra -Wno-missing-field-initializers -Wno-sign-compare -Wpointer-arith -Wall -Wno-unused -Wunused-value -Wunused-parameter -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-array-bounds C++ compiler: /bin/c++ GNU 4.8.5 C++ compiler flags: -march=core-avx2-Wextra -Wno-missing-field-initializers -Wpointer-arith -Wall -Wno-unused-function -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-array-bounds Boost version: 1.55.0 (internal) CUDA compiler: /usr/local/cuda/bin/nvcc nvcc: NVIDIA (R) Cuda compiler driver;Copyright (c) 2005-2016 NVIDIA Corporation;Built on Sun_Sep__4_22:14:01_CDT_2016;Cuda compilation tools, release 8.0, V8.0.44 CUDA compiler flags:-gencode;arch=compute_20,code=sm_20;-gencode;arch= compute_30,code=sm_30;-gencode;arch=compute_35,code= sm_35;-gencode;arch=compute_37,code=sm_37;-gencode;arch= compute_50,code=sm_50;-gencode;arch=compute_52,code= sm_52;-gencode;arch=compute_60,code=sm_60;-gencode;arch= compute_61,code=sm_61;-gencode;arch=compute_60,code= compute_60;-gencode;arch=compute_61,code=compute_61;-use_fast_math;; ;-march=core-avx2;-Wextra;-Wno-missing-field-initializers;-Wpointer-arith;- Wall;-Wno-unused-function;-O3;-DNDEBUG;-funroll-all-loops;- fexcess-precision=fast;-Wno-array-bounds; CUDA driver:8.0 CUDA runtime: 8.0 Running on 1 node with total 16 cores, 32 logical cores, 1 compatible GPU Hardware detected: CPU info: Vendor: GenuineIntel Brand: Intel(R) Xeon(R) CPU E5-2630 v3 @ 2.40GHz Family: 6 model: 63 stepping: 2 CPU features: aes apic avx avx2 clfsh cmov cx8 cx16 f16c fma htt lahf_lm mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdrnd rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic SIMD instructions most likely to fit this hardware: AVX2_256 SIMD instructions selected at GROMACS compile time: AVX2_256 GPU info: Number of GPUs detected: 1 #0: NVIDIA GeForce GTX 980 Ti, compute cap.: 5.2, ECC: no, stat: compatible Changing nstlist from 20 to 40, rlist from 1.2 to 1.2 Input Parameters: integrator = sd tinit = 0 dt = 0.002 nsteps = 100 init-step = 0 simulation-part= 1 comm-mode = Linear nstcomm= 100 bd-fric= 0 ld-seed= 57540858 emtol = 10 emstep = 0.01 niter = 20 fcstep = 0 nstcgsteep = 1000 nbfgscorr = 10 rtpi
Re: [gmx-users] Fwd: Relative free energy perturbation
I am apologize if I resend the same message but I forgot to change the object. Dear Hannes, Thank you very much for your reply, really appreciated. > Date: Mon, 26 Jun 2017 12:09:45 +0100 > From: Hannes Loeffler <hannes.loeff...@stfc.ac.uk> > To: <gromacs.org_gmx-users@maillist.sys.kth.se> > Cc: gmx-us...@gromacs.org > Subject: Re: [gmx-users] Fwd: Relative free energy perturbation > Message-ID: <20170626120945.75215...@stfc.ac.uk> > Content-Type: text/plain; charset="US-ASCII" > > On Mon, 26 Jun 2017 12:25:19 +0200 > Davide Bonanni <davide.bona...@unito.it> wrote: > > > 1) Can I perform the calculation in a single step with soft core > > potential enabled? I mean, is it correct to transform directly the > > hydrogen into a chlorine instead of using 2 topologys and 2 > > complexes, where in the first step I transform the hydrogen into > > dummy atom, and in the second I transform the dummy atom into > > chlorine. > > Technically speaking you can perfectly do that but in practice it can > be much more efficient to directly and linearly transform one atom type > into another (single topology approach). There is no need for a > softcore potential in this case. Those would only be activated for > atoms that either appear or disappear i.e. atoms with zero vdW > parameters. The input and topology files from FEsetup should be all > you need. Can I have problems if I keep active the softcore potential whether is not needed? > > 2) Referring to BevanLab Tutorial 6: Free Energy Calculation ( > > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gm > > x-tutorials/free_energy/index.html), I have to perform every step of > > molecular dynamics at every Lambda value, is that right? > > Yes, you will need to do a simulation for every and each lambda step. > > > > 3) I run a test minimization step (mdp file attached) of my complex > > at the last "init-lambda-state", 15 in my case. Looking at the .trr > > output file I can see that the bond between the carbon and the > > hydrogen which should be trasformed is longer than a normal C-H bond, > > but the atom is still recognized as hydrogen (picture > > "http://tinypic.com/r/2wp11dh/9": purple -> init-lambda-state = 0 ; > > blue -> init-lambda-state = 15). I was wondering if this is what I am > > supposed to see, so if gromacs is considering the state B of my > > system where I have chlorine bound to carbon instead hydrogen. > > What does "recognized as hydrogen" mean? I suspect that what you are > referring to is the output of some visualisation program because you > instructed it to interpret that particular atom to be a hydrogen. > > What you need to expect to see is that a C-H bond is transformed into a > C-Cl bond and accordingly the bond length increases. > Of course, It's like you said. I see the bond length increase as in the img "http://tinypic.com/r/2wp11dh/9;. Thank you again. Cheers, Davide Bonanni -- 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] gromacs.org_gmx-users Digest, Vol 158, Issue 165
Dear Hannes, Thank you very much for your reply, really appreciated. > Date: Mon, 26 Jun 2017 12:09:45 +0100 > From: Hannes Loeffler <hannes.loeff...@stfc.ac.uk> > To: <gromacs.org_gmx-users@maillist.sys.kth.se> > Cc: gmx-us...@gromacs.org > Subject: Re: [gmx-users] Fwd: Relative free energy perturbation > Message-ID: <20170626120945.75215...@stfc.ac.uk> > Content-Type: text/plain; charset="US-ASCII" > > On Mon, 26 Jun 2017 12:25:19 +0200 > Davide Bonanni <davide.bona...@unito.it> wrote: > > > 1) Can I perform the calculation in a single step with soft core > > potential enabled? I mean, is it correct to transform directly the > > hydrogen into a chlorine instead of using 2 topologys and 2 > > complexes, where in the first step I transform the hydrogen into > > dummy atom, and in the second I transform the dummy atom into > > chlorine. > > Technically speaking you can perfectly do that but in practice it can > be much more efficient to directly and linearly transform one atom type > into another (single topology approach). There is no need for a > softcore potential in this case. Those would only be activated for > atoms that either appear or disappear i.e. atoms with zero vdW > parameters. The input and topology files from FEsetup should be all > you need. Can I have problems if I keep active the softcore potential whether is not needed? > > 2) Referring to BevanLab Tutorial 6: Free Energy Calculation ( > > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gm > > x-tutorials/free_energy/index.html), I have to perform every step of > > molecular dynamics at every Lambda value, is that right? > > Yes, you will need to do a simulation for every and each lambda step. > > > > 3) I run a test minimization step (mdp file attached) of my complex > > at the last "init-lambda-state", 15 in my case. Looking at the .trr > > output file I can see that the bond between the carbon and the > > hydrogen which should be trasformed is longer than a normal C-H bond, > > but the atom is still recognized as hydrogen (picture > > "http://tinypic.com/r/2wp11dh/9": purple -> init-lambda-state = 0 ; > > blue -> init-lambda-state = 15). I was wondering if this is what I am > > supposed to see, so if gromacs is considering the state B of my > > system where I have chlorine bound to carbon instead hydrogen. > > What does "recognized as hydrogen" mean? I suspect that what you are > referring to is the output of some visualisation program because you > instructed it to interpret that particular atom to be a hydrogen. > > What you need to expect to see is that a C-H bond is transformed into a > C-Cl bond and accordingly the bond length increases. > Of course, It's like you said. I see the bond length to increase as in the img "http://tinypic.com/r/2wp11dh/9;. Thank you again. Cheers, Davide Bonanni -- 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] Fwd: Relative free energy perturbation
Hi, I am trying to perform an alchemical free energy perturbation with gromacs, since I am approaching this technique for the first time. So, it would be so nice if you could help me to clarify some doubt. I have built my system, which is composed of 1 protein, 2 cofactors, and 1 ligand that should changes from state A to B. I used FESetup to make the topology for my ligand. The change I want to apply to my molecule is just the transformation of a hydrogen into chlorine, so I do not have dummy atoms involved. This is the only string that changes from state A to B in my ligand topology: [Atoms] ; Nr type resnm atom cgnr chargemass typeB chargeB massB 30 h4 1 LIG H30 30 0.158051 1.0080 cl -0.078297 35.4500 So, I have the complex.gro and complex.top, I made some minimization tests and everything seems good. I have some doubts on the procedure I'm supposed to follow to perform FEP calculation. Some questions: 1) Can I perform the calculation in a single step with soft core potential enabled? I mean, is it correct to transform directly the hydrogen into a chlorine instead of using 2 topologys and 2 complexes, where in the first step I transform the hydrogen into dummy atom, and in the second I transform the dummy atom into chlorine. Using soft core potential I can perform any kind of transformation in single step, or are there some cases where I need to use different procedures? 2) Referring to BevanLab Tutorial 6: Free Energy Calculation ( http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gm x-tutorials/free_energy/index.html), I have to perform every step of molecular dynamics at every Lambda value, is that right? 3) I run a test minimization step (mdp file attached) of my complex at the last "init-lambda-state", 15 in my case. Looking at the .trr output file I can see that the bond between the carbon and the hydrogen which should be trasformed is longer than a normal C-H bond, but the atom is still recognized as hydrogen (picture "http://tinypic.com/r/2wp11dh/9": purple -> init-lambda-state = 0 ; blue -> init-lambda-state = 15). I was wondering if this is what I am supposed to see, so if gromacs is considering the state B of my system where I have chlorine bound to carbon instead hydrogen. I am apologize if my questions are technically incorrect. As I said it is the first time I'm approaching to free energy perturbation and every kind of help and suggestion is really appreciated. Thank you very much in advance. Best regards, Davide Bonanni ---------- Davide Bonanni, PhD student Dept. Science and Drug Technology University of Turin (UniTO) - Italy Mobile +39 3409726272 <+39%20340%20972%206272> -- -- 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.
