Re:Re: [gmx-users] MDRun -append error
Hi Roland,
Thanks for your reply. My log files are located in the same directory with
''traj.xtc', and the log files are readable by gromacs.
I have just find out the solution for my problem. That is because there were
also two backup log files named '#md_0_1.log#' and '#md_0_1.edr#' corresponding
to 'md_0_1.log' and 'md_0_1.edr'. These two files were generated for a trial
run. After removing the two files ('#md_0_1.log#' and '#md_0_1.edr#), gromacs
can restart successfully.
Thanks for your reply!
best regards
Xianqiang
--
Xianqiang Sun
Email: xianqi...@theochem.kth.se
Division of Theoretical Chemistry and Biology
School of Biotechnology
Royal Institute of Technology
S-106 91 Stockholm, Sweden
在 2011-11-17 09:12:25，Roland Schulz rol...@utk.edu 写道：
On Wed, Nov 16, 2011 at 4:11 PM, xianqiang xianqiang...@126.com wrote:
Hi, all
I just restart a simulation with 'mpirun -np 8 mdrun -pd yes -s md_0_1.tpr -cpi
state.cpt -append'
However, the following error appears:
Output file appending has been requested,
but some output files listed in the checkpoint file state.cpt
are not present or are named differently by the current program:
output files present: traj.xtc
output files not present or named differently: md_0_1.log md_0_1.edr
---
Program mdrun, VERSION 4.5.3
Source code file: ../../../gromacs-4.5.3/src/gmxlib/checkpoint.c, line: 2139
Fatal error:
File appending requested, but only 1 of the 3 output files are present
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
The two files which can not be found were located in the same directory with
'traj.xtc', and why they can not be found by gromacs?
Maybe they are not readable? Can you look at the log file (e.g. using less)?
Roland
Thanks and best regards,
Xianqiang
--
Xianqiang Sun
Email: xianqi...@theochem.kth.se
Division of Theoretical Chemistry and Biology
School of Biotechnology
Royal Institute of Technology
S-106 91 Stockholm, Sweden
--
ORNL/UT Center for Molecular Biophysics cmb.ornl.gov
865-241-1537, ORNL PO BOX 2008 MS6309
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[gmx-users] Strange problem.complex out of Box after EM
Dear Gromacs users I am trying to simulate a protein complex. That complex has been obtained after protein-protein docking. I have geneated topology, defined box and solvate, added ions successfully. My complex is centered in box. but when I performed Energy minimization then my protein complex comes out of box from one side. can any body help me in fixing this problem so that i could proceed towards equilibrium steps.. Many thanks with anticipation Regards Saba -- Saba Ferdous Research Scholar (M. Phil) National Center for Bioinformatics Quaid-e-Azam University, Islamabad Pakistan -- 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] gromacs/mopac compilation: linking libmopac
Hi all I post here the present status of my query in case my findings may be helpful for someone else. In the case B (using gfortran to compile libmopac) I have some success building g the gromacs binary for mdrun in my x86_64 system. **A Regarding the compilation with ifort, making test with simple C code I relized that (at least in my case), it is needed to add some extra intel libreries during compilation. Concretely I added the mkl libraries (maybe libm was enough, but just in case) and the additional libraries libifcore, libifcore_pic, libimf, libifport and libintlc (actually the two that seem strongly required were libifcore and libintlc). The case is that libintlc is only available in shared version, so I fist recompiled my libmopac library with -fPIC flag: ifort -O2 -fPIC -c *f; ar rcv libmopac.a *.o; ranlib libifmopac.a In my test C simple program, it was possible to link against the static libifmopac.a while using other shared libraries (omitting the flag -static), so I used --enable-shared. The configure script was subsequently called as follows (with double precision as well): ./configure --prefix /home/cerezo/Programas/gromacs-4.5.5_with_ifort_mopac/ --program-suffix=_d_ifmopac LDFLAGS=-L/home/cerezo/lib -L/home/cerezo/lib/fftw/lib -L/usr/share/intel/mkl/lib/intel64 -L/usr/share/intel/lib/intel64 CPPFLAGS=-DUSE_MOPAC -I/home/cerezo/lib/fftw/include --with-qmmm-mopac LIBS=-lmkl_intel_ilp64 -lmkl_core -lmkl_sequential -lifcore -lifcore_pic -limf -lirc -lifport -lintlc -lifmopac --disable-threads --disable-float LD_LIBRARY_PATH=/usr/share/intel/mkl/lib/intel64:/usr/share/intel/lib/intel64::LD_LIBRARY_PATH Then make mdrun -j 4 gave the following error: cc -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -msse2 -funroll-all-loops -std=gnu99 -fexcess-precision=fast -o .libs/mdrun gctio.o ionize.o do_gct.o repl_ex.o xutils.o runner.o md.o mdrun.o genalg.o md_openmm.o -L/home/cerezo/lib -L/home/cerezo/lib/fftw/lib -L/usr/share/intel/mkl/lib/intel64 -L/usr/share/intel/lib/intel64 ./.libs/libgmxpreprocess_d.so /home/cerezo/Programas/src/GROMACS_vX/gromacs-4.5.5/src/mdlib/.libs/libmd_d.so ../mdlib/.libs/libmd_d.so /home/cerezo/lib/fftw/lib/libfftw3.so /home/cerezo/Programas/src/GROMACS_vX/gromacs-4.5.5/src/gmxlib/.libs/libgmx_d.so ../gmxlib/.libs/libgmx_d.so -lnsl -lm -lmkl_intel_ilp64 -lmkl_core -lmkl_sequential -lifcore -lifcore_pic -limf -lirc -lifport -lintlc -lifmopac -Wl,--rpath -Wl,/home/cerezo/Programas/gromacs-4.5.5_with_ifort_mopac/lib -Wl,--rpath -Wl,/home/cerezo/lib/fftw/lib /home/cerezo/Programas/src/GROMACS_vX/gromacs-4.5.5/src/mdlib/.libs/libmd_d.so: undefined reference to `__svml_asin2' /home/cerezo/Programas/src/GROMACS_vX/gromacs-4.5.5/src/mdlib/.libs/libmd_d.so: undefined reference to `__svml_exp2_mask' collect2: ld returned 1 exit status make[1]: *** [mdrun] Error 1 make[1]: se sale del directorio «/home/cerezo/Programas/src/GROMACS_vX/gromacs-4.5.5/src/kernel» **B I succeeded to build gromacs/mopac with gfortran compiled libmopac. Fisrt I compiled libmopac with: gfortran -std=legacy -c *.f; ar rcv libmopac.a *.o; ranlib libmopac.a (I made the necessary changes to remove the warnings and errors, such as changing the calls to SECOND(1) by SECOND() in polar.f and writmo.f) In this case, gfortran procedures are simply linked with a single library: libgfortran, with static version. Thus, I deactivated shared option in the configure script. Then, the configure script for gromacs looked like: ./configure --prefix /home/cerezo/Programas/gromacs-4.5.5_with_gfor_mopac/ --program-suffix=_d_mopac LDFLAGS=-L/home/cerezo/lib -L/home/cerezo/lib/fftw/lib CPPFLAGS=-DUSE_MOPAC -I/home/cerezo/lib/fftw/include --with-qmmm-mopac LIBS=-lmopac -lgfortran --disable-threads --disable-float -disable-shared make mdrun -j 4 make install-mdrun All worked correctly. However, I got a segmentation fault when running a qm/mm calculation, the problem originated at libmopac subroutines. Actually, the problem is in the subroutine FOCK2 (in fock2.f), at least in my system compiling with gfortran: GNU Fortran (Ubuntu/Linaro 4.5.2-8ubuntu4) 4.5.2. The work around comes as follows: In fock2.f: Line 35: IF(ICALCN.NE.NUMCAL) THEN [This if loop assures that variable initialization is only made the fisrt time the main program calls the subroutine. However, in my gfortran compiled binary, the variables were not saved from calls. So I capped this loop (is should end at line 89), so that now it looks like:] Line 35:IF(ICALCN.NE.NUMCAL) THEN Line 36: ICALCN=NUMCAL Line 37(new): ENDIF [this was moved from line 89] And now I could run gromacs/mopac without errors. I guess with another compiler, this problem will not arise, but at least here is a solution for (standard?) gfortran in a x86_64 system Javier El 10/11/11 14:35, Javier Cerezo escribió: Hi all I am trying to compile gromacs
[gmx-users] Regarding TIP4P structure
Dear all, Could anybody send me the link for getting the tip4p tip3p and tip5p single water structure in gro/pdb or in anyother format. Thank you. *With Regards, Ravi Kumar Venkatraman, IPC Dept., IISc, Bangalore, INDIA. +91-9686933963.* -- 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] gromacs/mopac compilation: linking libmopac (Javier Cerezo)
, Could anybody send me the link for getting the tip4p tip3p and tip5p single water structure in gro/pdb or in anyother format. Thank you. *With Regards, Ravi Kumar Venkatraman, IPC Dept., IISc, Bangalore, INDIA. +91-9686933963.* -- next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/2017/4840f654/attachment.html -- -- gmx-users mailing list gmx-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! End of gmx-users Digest, Vol 91, Issue 117 ** -- 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] gromacs/mopac compilation: linking libmopac (Javier Cerezo)
] Regarding TIP4P structure To: gmx-users@gromacs.org Message-ID: ca+c-nqzzdjz25rkkl5qdun-7snby6p5sacp7zjzlt_vvp3p...@mail.gmail.com Content-Type: text/plain; charset=iso-8859-1 Dear all, Could anybody send me the link for getting the tip4p tip3p and tip5p single water structure in gro/pdb or in anyother format. Thank you. *With Regards, Ravi Kumar Venkatraman, IPC Dept., IISc, Bangalore, INDIA. +91-9686933963.* -- next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/2017/4840f654/attachment.html -- -- gmx-users mailing list gmx-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! End of gmx-users Digest, Vol 91, Issue 117 ** -- Javier CEREZO BASTIDA PhD Student Physical Chemistry Universidad de Murcia Murcia (Spain) Tlf.(+34)868887434 -- 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] Regarding cosine content
Hello all, I have done PCA from 50ns long trajectory for two similar proteins (length 180 aa and RMSD 0.2 A). The equilibration time and final simulation condition were identical for both the protein. But when I checked the cosine content for PC1 for both proteins they were 0.9 and 0.5 respectively. What can be the reason for this huge difference in cosine content of the two proteins ? -- --- Regards, Bipin Singh -- 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] Strange problem.complex out of Box after EM
Saba Ferdous wrote: Dear Gromacs users I am trying to simulate a protein complex. That complex has been obtained after protein-protein docking. I have geneated topology, defined box and solvate, added ions successfully. My complex is centered in box. but when I performed Energy minimization then my protein complex comes out of box from one side. can any body help me in fixing this problem so that i could proceed towards equilibrium steps.. There is no problem. It is odd that EM would cause periodicity issues, but suggests that your protein is not centered properly or that your box is not large enough to accommodate it. There may be some inconvenience for visualization (which can be fixed), but there is no such thing as outside in a periodic system. http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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] Re: Umbrella Sampling - Justin tutorial
Hi Justin, I am sorry for so many questions but I do not understand something. First we run the simulation of pulling Chain A from ChainB with constant force (pull_k1=1000) and constant velocity of pulling (pull_rate1=0.01) We extract windows as we discussed and then run simulations with those configurations as a starting point. I saw the trajectory of one of these simulations and it looks like normal MD simulation. My question is: Why do we have in mdp file still pull code as we do not pull protein chain any more? Pull rate is set to zero but force is still applied... why? Is this code just used to extract pullf.xvg and pullx.xvg which does not change too much? I would appreciate the explanation as without undesratnding the basics its not good to do any simulation like this. Thank you Steven Are my questions to trivial or noones knows? Please, help! On Wed, Nov 16, 2011 at 9:31 AM, Steven Neumann s.neuman...@gmail.comwrote: Hi GMX Users, I am doing Justin tutorial of Umbrella sampling. I have just finished continous pulling of chainA from the reference chainB. I have some questions. I looked at the trajectory of pulling and it has began with dissociating residue 27Alanine from the ChainB following 26, 25, 24...1. My question is why? As you apply pulling with the constant force to the COM of the whole chain why does it start with terminal residue following then one by one? Why not the middle one or any other? The second thing I would like to extract starting configurations from from my pulling. Till frame 189 the COM varies from 0.49 to 0.56 - makes sense as the ChainA is still within ChainB. I would like to use configurations: 0 - 0.50 50 - 0.52 100 - 0.51 150 - 0.51 200 - 0.62 250 - 2.21 500 - 5.48 My question is: Do I have to use exactly the same e.g. 0.2 nm spacing or this configuration above is ok? Can the spacing in nm vary? And the last thing - is it required to use frames till 189 as the COM varies in this area? Thank you! Steven -- 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] Regarding cosine content
Hi Bipin, It seems one of the proteins is taking longer to reach an equilibrium. Maybe it is undergoing a conformational change? Did you calculate the principal components per protein, or for the joint trajectories? It would have been better to echo the commands you used on the list, because it might result in a different interpretation. I also made some comments on the list a short while ago regarding the interpretation of projections and cosine content. Maybe they can help you form a picture of what is happening :) Hope it helps, Tsjerk On Thu, Nov 17, 2011 at 12:22 PM, bipin singh bipinel...@gmail.com wrote: Hello all, I have done PCA from 50ns long trajectory for two similar proteins (length 180 aa and RMSD 0.2 A). The equilibration time and final simulation condition were identical for both the protein. But when I checked the cosine content for PC1 for both proteins they were 0.9 and 0.5 respectively. What can be the reason for this huge difference in cosine content of the two proteins ? -- --- Regards, Bipin Singh -- gmx-users mailing list gmx-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 -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- 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] Regarding cosine content
Thanks for the reply... I calculated principal components per protein using the command g_anaeig -f md.xtc -s md.tpr -v eigenvec.trr -eig eigenval.xvg -comp eigcomp.xvg -rmsf eigrmsf.xvg -2d 2dproj.xvg -proj proj.xvg -tu ns -extr extr.pdb -filt filt.xtc -first 1 -last 2 Also please suggest how one can differentiate between the two scenarios, when the high cosine content is due to random diffusion or conformational changes ? On Thu, Nov 17, 2011 at 17:34, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Bipin, It seems one of the proteins is taking longer to reach an equilibrium. Maybe it is undergoing a conformational change? Did you calculate the principal components per protein, or for the joint trajectories? It would have been better to echo the commands you used on the list, because it might result in a different interpretation. I also made some comments on the list a short while ago regarding the interpretation of projections and cosine content. Maybe they can help you form a picture of what is happening :) Hope it helps, Tsjerk On Thu, Nov 17, 2011 at 12:22 PM, bipin singh bipinel...@gmail.com wrote: Hello all, I have done PCA from 50ns long trajectory for two similar proteins (length 180 aa and RMSD 0.2 A). The equilibration time and final simulation condition were identical for both the protein. But when I checked the cosine content for PC1 for both proteins they were 0.9 and 0.5 respectively. What can be the reason for this huge difference in cosine content of the two proteins ? -- --- Regards, Bipin Singh -- gmx-users mailing list gmx-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 -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- gmx-users mailing list gmx-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 -- --- Regards, Bipin Singh -- 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] Cuda not detected
Hey, I am playing with the gpu version of mdrun and could make it run with: ~/gromacs/gpu/bin/mdrun-gpu -s topol.tpr -device OpenMM:platform=Cuda,memtest=15,deviceid=0,force-device=yes However after reboot of the machine ( which is a testing machine) I get the following error: --- Program mdrun-gpu, VERSION 4.5.5 Source code file: /home/weber/gromacs/gromacs-4.5.5_gpu/src/kernel/ openmm_wrapper.cpp, line: 1272 Fatal error: The requested platform Cuda could not be found. echo $LD_LIBRARY_PATH:/opt/software/ganglia-3.1.7/lib64:/opt/software/ htop-0.8.3:/usr/local/cuda/lib64:/usr/local/cuda/lib:/home/weber/ OpenMM3.1.1-Linux64/lib echo $PATH/usr/local/bin:/usr/bin:/bin:/usr/X11R6/bin:/usr/games:/usr/ lib64/jvm/jre/bin:/opt/software/nvidia/3.2.16/cuda/bin:/opt/software/ ganglia-3.1.7/bin:/opt/software/htop-0.8.3/bin:/usr/lib/mit/bin:/usr/ lib/mit/sbin:.:/usr/local/cuda/bin:/home/weber/cmake-2.8.6/bin I run a simple gpu test program and it works. I believe something is not linked correctly, maybe someone can give me a hint. Thank You Andrzej -- 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] Regarding TIP4P structure
Ravi Kumar Venkatraman wrote: Dear all, Could anybody send me the link for getting the tip4p tip3p and tip5p single water structure in gro/pdb or in anyother format. A single water molecule? Copy and paste the coordinates from the existing .gro files in $GMXLIB. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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] Re: Umbrella Sampling - Justin tutorial
Steven Neumann wrote: Hi Justin, I am sorry for so many questions but I do not understand something. First we run the simulation of pulling Chain A from ChainB with constant force (pull_k1=1000) and constant velocity of pulling (pull_rate1=0.01) We extract windows as we discussed and then run simulations with those configurations as a starting point. I saw the trajectory of one of these simulations and it looks like normal MD simulation. My question is: Why do we have in mdp file still pull code as we do not pull protein chain any more? Pull rate is set to zero but force is still applied... why? Is this code just used to extract pullf.xvg and pullx.xvg which does not change too much? I would appreciate the explanation as without undesratnding the basics its not good to do any simulation like this. Have you read the WHAM paper, or the one specific for g_wham, or perhaps papers about umbrella sampling in general? You should start there before diving in to doing the simulations. The harmonic force applied in the SMD and US simulations is simply a biasing force to make something happen. With a non-zero pull_rate, motion in a particular direction is forced to happen. With a pull_rate of zero, the COM distance is simply restricted - the biasing force maintains the COM distance between the two defined species, while allowing it to oscillate according to a harmonic force defined by pull_k1. Thus you establish sampling overlap between neighboring windows along the reaction coordinate. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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] Cuda not detected
try nvidia-smi -a to see whether the GPU card has been correctly configured. This happens on my GPU node. Every time I reboot the computer, I must reconfigure the GPU cards with nvidia-smi -a using root account. Ye 2011-11-17 From： Andrzej Rzepiela Date： 2011-11-17 21:01:07 To： gmx-users CC： Subject： [gmx-users] Cuda not detected Hey, I am playing with the gpu version of mdrun and could make it run with: ~/gromacs/gpu/bin/mdrun-gpu -s topol.tpr -device OpenMM:platform=Cuda,memtest=15,deviceid=0,force-device=yes However after reboot of the machine ( which is a testing machine) I get the following error: --- Program mdrun-gpu, VERSION 4.5.5 Source code file: /home/weber/gromacs/gromacs-4.5.5_gpu/src/kernel/ openmm_wrapper.cpp, line: 1272 Fatal error: The requested platform Cuda could not be found. echo $LD_LIBRARY_PATH:/opt/software/ganglia-3.1.7/lib64:/opt/software/ htop-0.8.3:/usr/local/cuda/lib64:/usr/local/cuda/lib:/home/weber/ OpenMM3.1.1-Linux64/lib echo $PATH/usr/local/bin:/usr/bin:/bin:/usr/X11R6/bin:/usr/games:/usr/ lib64/jvm/jre/bin:/opt/software/nvidia/3.2.16/cuda/bin:/opt/software/ ganglia-3.1.7/bin:/opt/software/htop-0.8.3/bin:/usr/lib/mit/bin:/usr/ lib/mit/sbin:.:/usr/local/cuda/bin:/home/weber/cmake-2.8.6/bin I run a simple gpu test program and it works. I believe something is not linked correctly, maybe someone can give me a hint. Thank You Andrzej -- 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] Gromacs 3D maps
Dear all, I'd like to transform an md gromacs trajectory in a 3d maps set. I mean that every 100ps, I need to export frame coordinates to a 3d map. Than I need to compare a map with the following. Could give me any advice about tools/software to use? Additionally I need to export the coordinate (x,y,z) of atom's protein, deriving from MD trajectory, to a matrix where each columns are frame number, 1-n atoms'positions (x,y,z coordinates). Any suggestion? Thanks in advance -- 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] Re: Umbrella Sampling - Justin tutorial
Thank you Justin, I will read it for sure and come back to my simulations! Steven On Thu, Nov 17, 2011 at 1:25 PM, Justin A. Lemkul jalem...@vt.edu wrote: Steven Neumann wrote: Hi Justin, I am sorry for so many questions but I do not understand something. First we run the simulation of pulling Chain A from ChainB with constant force (pull_k1=1000) and constant velocity of pulling (pull_rate1=0.01) We extract windows as we discussed and then run simulations with those configurations as a starting point. I saw the trajectory of one of these simulations and it looks like normal MD simulation. My question is: Why do we have in mdp file still pull code as we do not pull protein chain any more? Pull rate is set to zero but force is still applied... why? Is this code just used to extract pullf.xvg and pullx.xvg which does not change too much? I would appreciate the explanation as without undesratnding the basics its not good to do any simulation like this. Have you read the WHAM paper, or the one specific for g_wham, or perhaps papers about umbrella sampling in general? You should start there before diving in to doing the simulations. The harmonic force applied in the SMD and US simulations is simply a biasing force to make something happen. With a non-zero pull_rate, motion in a particular direction is forced to happen. With a pull_rate of zero, the COM distance is simply restricted - the biasing force maintains the COM distance between the two defined species, while allowing it to oscillate according to a harmonic force defined by pull_k1. Thus you establish sampling overlap between neighboring windows along the reaction coordinate. -Justin -- ==**== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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
[gmx-users] user contribution
Hallo all, how can I upload a molecule topology? I registered as a user but when I click at the attache file link this page cannot be changed appears. Thanks in advance for your help. Thorsten -- 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] calculate potential with tabulated non-bonded interactions
Dear all, I am trying to calculate potentials for RNA structures with a serial of tabulated potentials (non-bonded). And the only potential I am going to use is the tabulated potentials, and the effect from force field should be removed. However, when I use pdb2gmx to build the topology file, I have to choose a force field. What should I do for that? Thanks. -- Best, Liang Liu -- 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] Cuda not detected
On 11/17/11 10:10 PM, Andrzej Rzepiela wrote: Hey, thank you for the hint. I just finished the tests. The machine is Intel xeon R, 12 cores , 4 Teslas M2090 and 96 gb of memory. I used the most demanding PME dhfr benchmark system ( 7000w + protein) and obtained the following results: 1 cpu core run: 2.135 ns a day 12 cpu cores run: 21.478 ns a day 1 gpu unit run ( how many cpu cores are used, one ? ): 13.0 ns/day 4 parallel gpu runs on the node, performance: 12.884, 10.296, 8.290 and 6.953 ns/day, which is on average about 9.6 ns for one gpu. From your experience, are this expected numbers ? From the benchmarks on the website I had e feeling that the gpu runs will be faster. GPU is faster with implicit solvent and other constraints up to now. They are optimizing everything for the next version of gromacs http://www.gromacs.org/Developer_Zone/Roadmap/GROMACS_4.6 More detailed info on the gromacs manual. -- Gianluca Santoni, Institut de Biologie Structurale 41 rue Horowitz Grenoble _ Please avoid sending me Word or PowerPoint attachments. See http://www.gnu.org/philosophy/no-word-attachments.html -- 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] calculate potential with tabulated non-bonded interactions
Liu, Liang wrote: Dear all, I am trying to calculate potentials for RNA structures with a serial of tabulated potentials (non-bonded). And the only potential I am going to use is the tabulated potentials, and the effect from force field should be removed. However, when I use pdb2gmx to build the topology file, I have to choose a force field. What should I do for that? Thanks. It sounds like you need to be constructing your own force field, completely, from scratch. If you're not looking to use the existing force fields, this sounds like the only real solution. You can take the time to make .xvg files for bonded and nonbonded interactions (see the manual), but that is probably just as much work and your simulations will be much slower. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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] calculate potential with tabulated non-bonded interactions
Well, I already have the xvg files from others. However I don't know how to use it. On Thu, Nov 17, 2011 at 10:00 AM, Justin A. Lemkul jalem...@vt.edu wrote: Liu, Liang wrote: Dear all, I am trying to calculate potentials for RNA structures with a serial of tabulated potentials (non-bonded). And the only potential I am going to use is the tabulated potentials, and the effect from force field should be removed. However, when I use pdb2gmx to build the topology file, I have to choose a force field. What should I do for that? Thanks. It sounds like you need to be constructing your own force field, completely, from scratch. If you're not looking to use the existing force fields, this sounds like the only real solution. You can take the time to make .xvg files for bonded and nonbonded interactions (see the manual), but that is probably just as much work and your simulations will be much slower. -Justin -- ==**== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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 -- Best, Liang Liu -- 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] calculate potential with tabulated non-bonded interactions
Liu, Liang wrote: Well, I already have the xvg files from others. However I don't know how to use it. Start with the manual, where modifications to the topology and relevant commands and files are described. Then refer to the how-to online, which has specific instructions. Then, ask specific questions of problems you are having. I doubt anyone on this list will be able or willing to guess where your problems are at this point. -Justin On Thu, Nov 17, 2011 at 10:00 AM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Liu, Liang wrote: Dear all, I am trying to calculate potentials for RNA structures with a serial of tabulated potentials (non-bonded). And the only potential I am going to use is the tabulated potentials, and the effect from force field should be removed. However, when I use pdb2gmx to build the topology file, I have to choose a force field. What should I do for that? Thanks. It sounds like you need to be constructing your own force field, completely, from scratch. If you're not looking to use the existing force fields, this sounds like the only real solution. You can take the time to make .xvg files for bonded and nonbonded interactions (see the manual), but that is probably just as much work and your simulations will be much slower. -Justin -- ==__== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 tel:%28540%29%20231-9080 http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==__== -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/__mailman/listinfo/gmx-users http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/__Support/Mailing_Lists/Search 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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/__Support/Mailing_Lists http://www.gromacs.org/Support/Mailing_Lists -- Best, Liang Liu -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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] GROMACS/ORCA QMMM
Hi Cristoph, Thanks for the reply. I found that my problem was not gromacs. The input that ORCA was receiving from GROMACS did not have the correct number of hydrogens. I've solved this problem now and ORCA is running fine. I however ran into another problem with my energy minimization. The output from my gromacs log file is the following: Step Time Lambda 00.00.0 Energies (kJ/mol) Bond AngleProper Dih. Improper Dih. LJ-14 1.21899e+041.92496e+035.62567e+031.49141e+013.68001e+03 Coulomb-14LJ (SR) Coulomb (SR) Coul. recip.Quantum En. 2.41200e+041.47494e+05 -5.06544e+05 -7.56009e+04 -3.96508e+06 Potential Pressure (bar) -4.35218e+06 -2.10629e+04 Step Time Lambda 11.00.0 Energies (kJ/mol) Bond AngleProper Dih. Improper Dih. LJ-14 1.20006e+041.92297e+035.62600e+031.47801e+013.67746e+03 Coulomb-14LJ (SR) Coulomb (SR) Coul. recip.Quantum En. 2.41174e+041.46421e+05 -5.06609e+05 -7.56156e+04 -4.00402e+06 Potential Pressure (bar) -4.39246e+06 -2.10739e+04 Step Time Lambda 22.00.0 Energies (kJ/mol) Bond AngleProper Dih. Improper Dih. LJ-14 1.17961e+041.92126e+035.62633e+031.46477e+013.67461e+03 Coulomb-14LJ (SR) Coulomb (SR) Coul. recip.Quantum En. 2.41145e+041.45528e+05 -5.06679e+05 -7.56315e+04 -4.18671e+06 Potential Pressure (bar) -4.57635e+06 -2.10854e+04 Step Time Lambda 33.00.0 Step Time Lambda 44.00.0 Energies (kJ/mol) Bond AngleProper Dih. Improper Dih. LJ-14 1.16705e+041.92041e+035.62652e+031.45728e+013.67282e+03 Coulomb-14LJ (SR) Coulomb (SR) Coul. recip.Quantum En. 2.41128e+041.45113e+05 -5.06721e+05 -7.56410e+04 -4.24486e+06 Potential Pressure (bar) -4.63509e+06 -2.10913e+04 Step Time Lambda 55.00.0 Step Time Lambda 66.00.0 Step Time Lambda 77.00.0 Step Time Lambda 88.00.0 Step Time Lambda 99.00.0 Step Time Lambda 10 10.00.0 Step Time Lambda 11 11.00.0 Step Time Lambda 12 12.00.0 Step Time Lambda 13 13.00.0 Step Time Lambda 14 14.00.0 Step Time Lambda 15 15.00.0 Step Time Lambda 16 16.00.0 Step Time Lambda 17 17.00.0 Step Time Lambda 18 18.00.0 Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax 1000 Double precision normally gives you higher accuracy. You might need to increase your constraint accuracy, or turn off constraints alltogether (set constraints = none in mdp file) Why doesn't GROMACS output the energies for certain steps? Step 3 and steps 5-18 do show any output in the log file. Any ideas why this is happening? Thanks, Jose Tusell On Mon, Nov 14, 2011 at 7:05 AM, Christoph Riplinger c...@thch.uni-bonn.de wrote: Dear Jose, I tried oniom which stopped for me either (although without a segfault). Have you tried QMMMscheme normal? Christoph On 11/11/2011 05:53 PM, Jose Tusell wrote: Dear GROMACS users, I'm trying to run a QM-MM optimization. I solvate my protein and add ions then I do a classical optimization (just GROMACS). After that I run grompp with the following minim.mdp file (just showing qmmm options): QMMM = yes QMMM-grps = Other QMmethod = RHF QMbasis = 3-21G QMMMscheme = Oniom QMcharge = -1 QMmult = 1 SH = no This creates the *.tpr file that use to run mdrun. I use the following *.ORCAINFO file: !PAL8 Quick-DFT VerySlowConv %scf Maxiter 300 end %pal nprocs 8
Re: [gmx-users] Strange problem.complex out of Box after EM
Please change the subject line to the relevant topic and do not paste the entire digest. I guess the archive is already somewhat hopeless, but let's not make it worse :) Saba Ferdous wrote: Dear Justin, I have set 1.5 dodecahedron. i centered the complex in box. complex.gro, complexsol.gro and complex_sol_ions.gro seems inside in box. I m using VMD for visualization. i have rotated it in 3D while when after EM step, i visualize em.gro then half complex seems outside the box. is there any way to center em.gro after energy minimization? Again, this is just a matter of visualization. There is nothing wrong and nothing needed to fix. You can rewrap the periodic cell with trjconv -pbc mol -ur compact if you find you want more convenient visualization. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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] calculate potential with tabulated non-bonded interactions
Liu, Liang wrote: Well my first question is: if the pdb2gmx command must take a force file? I guess it should be necessary. Then the available list contains amber and others, but not user-specified potential. This will affect the future simulation or calculation? Yes. Gromacs allows you provide tabulated potentials for van der Waals and Coulombic interactions (nonbonded), as well as bonded terms. The complication is that force fields are somewhat more complex than that. For instance, there are intramolecular terms (such as 1-4 interactions) that may or may not be scaled, depending on the force field used. If you have a completely custom force field and you are trying to override all elements of an existing force field, it is better to simply write a new force field rather than attempt to hack an old one. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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] GROMACS/ORCA QMMM
Jose Tusell wrote: Hi Cristoph, Thanks for the reply. I found that my problem was not gromacs. The input that ORCA was receiving from GROMACS did not have the correct number of hydrogens. I've solved this problem now and ORCA is running fine. I however ran into another problem with my energy minimization. The output from my gromacs log file is the following: Step Time Lambda 00.00.0 Energies (kJ/mol) Bond AngleProper Dih. Improper Dih. LJ-14 1.21899e+041.92496e+035.62567e+031.49141e+013.68001e+03 Coulomb-14LJ (SR) Coulomb (SR) Coul. recip.Quantum En. 2.41200e+041.47494e+05 -5.06544e+05 -7.56009e+04 -3.96508e+06 Potential Pressure (bar) -4.35218e+06 -2.10629e+04 Step Time Lambda 11.00.0 Energies (kJ/mol) Bond AngleProper Dih. Improper Dih. LJ-14 1.20006e+041.92297e+035.62600e+031.47801e+013.67746e+03 Coulomb-14LJ (SR) Coulomb (SR) Coul. recip.Quantum En. 2.41174e+041.46421e+05 -5.06609e+05 -7.56156e+04 -4.00402e+06 Potential Pressure (bar) -4.39246e+06 -2.10739e+04 Step Time Lambda 22.00.0 Energies (kJ/mol) Bond AngleProper Dih. Improper Dih. LJ-14 1.17961e+041.92126e+035.62633e+031.46477e+013.67461e+03 Coulomb-14LJ (SR) Coulomb (SR) Coul. recip.Quantum En. 2.41145e+041.45528e+05 -5.06679e+05 -7.56315e+04 -4.18671e+06 Potential Pressure (bar) -4.57635e+06 -2.10854e+04 Step Time Lambda 33.00.0 Step Time Lambda 44.00.0 Energies (kJ/mol) Bond AngleProper Dih. Improper Dih. LJ-14 1.16705e+041.92041e+035.62652e+031.45728e+013.67282e+03 Coulomb-14LJ (SR) Coulomb (SR) Coul. recip.Quantum En. 2.41128e+041.45113e+05 -5.06721e+05 -7.56410e+04 -4.24486e+06 Potential Pressure (bar) -4.63509e+06 -2.10913e+04 Step Time Lambda 55.00.0 Step Time Lambda 66.00.0 Step Time Lambda 77.00.0 Step Time Lambda 88.00.0 Step Time Lambda 99.00.0 Step Time Lambda 10 10.00.0 Step Time Lambda 11 11.00.0 Step Time Lambda 12 12.00.0 Step Time Lambda 13 13.00.0 Step Time Lambda 14 14.00.0 Step Time Lambda 15 15.00.0 Step Time Lambda 16 16.00.0 Step Time Lambda 17 17.00.0 Step Time Lambda 18 18.00.0 Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax 1000 Double precision normally gives you higher accuracy. You might need to increase your constraint accuracy, or turn off constraints alltogether (set constraints = none in mdp file) Why doesn't GROMACS output the energies for certain steps? Step 3 and steps 5-18 do show any output in the log file. Any ideas why this is happening? This happens for the reasons printed by mdrun - those steps caused no change in energy. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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] Regarding Shell Molecular Dynamics
Dear All, Is it not possible to minimize using cg with flexible constraints? Thank you In advance. *With Regards, Ravi Kumar Venkatraman, IPC Dept., IISc, Bangalore, INDIA. +91-9686933963.* -- 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] GROMACS/ORCA QMMM
Hi Justin, Thanks for the input on why this is happening. It sounds a little suspicious that the energy doesn't change after a few steps of energy minimization. Do you know of any way that I can find out what is going on? Thanks, Jose Tusell On Thu, Nov 17, 2011 at 10:58 AM, Justin A. Lemkul jalem...@vt.edu wrote: Jose Tusell wrote: Hi Cristoph, Thanks for the reply. I found that my problem was not gromacs. The input that ORCA was receiving from GROMACS did not have the correct number of hydrogens. I've solved this problem now and ORCA is running fine. I however ran into another problem with my energy minimization. The output from my gromacs log file is the following: Step Time Lambda 0 0.0 0.0 Energies (kJ/mol) Bond Angle Proper Dih. Improper Dih. LJ-14 1.21899e+04 1.92496e+03 5.62567e+03 1.49141e+01 3.68001e+03 Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip. Quantum En. 2.41200e+04 1.47494e+05 -5.06544e+05 -7.56009e+04 -3.96508e+06 Potential Pressure (bar) -4.35218e+06 -2.10629e+04 Step Time Lambda 1 1.0 0.0 Energies (kJ/mol) Bond Angle Proper Dih. Improper Dih. LJ-14 1.20006e+04 1.92297e+03 5.62600e+03 1.47801e+01 3.67746e+03 Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip. Quantum En. 2.41174e+04 1.46421e+05 -5.06609e+05 -7.56156e+04 -4.00402e+06 Potential Pressure (bar) -4.39246e+06 -2.10739e+04 Step Time Lambda 2 2.0 0.0 Energies (kJ/mol) Bond Angle Proper Dih. Improper Dih. LJ-14 1.17961e+04 1.92126e+03 5.62633e+03 1.46477e+01 3.67461e+03 Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip. Quantum En. 2.41145e+04 1.45528e+05 -5.06679e+05 -7.56315e+04 -4.18671e+06 Potential Pressure (bar) -4.57635e+06 -2.10854e+04 Step Time Lambda 3 3.0 0.0 Step Time Lambda 4 4.0 0.0 Energies (kJ/mol) Bond Angle Proper Dih. Improper Dih. LJ-14 1.16705e+04 1.92041e+03 5.62652e+03 1.45728e+01 3.67282e+03 Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip. Quantum En. 2.41128e+04 1.45113e+05 -5.06721e+05 -7.56410e+04 -4.24486e+06 Potential Pressure (bar) -4.63509e+06 -2.10913e+04 Step Time Lambda 5 5.0 0.0 Step Time Lambda 6 6.0 0.0 Step Time Lambda 7 7.0 0.0 Step Time Lambda 8 8.0 0.0 Step Time Lambda 9 9.0 0.0 Step Time Lambda 10 10.0 0.0 Step Time Lambda 11 11.0 0.0 Step Time Lambda 12 12.0 0.0 Step Time Lambda 13 13.0 0.0 Step Time Lambda 14 14.0 0.0 Step Time Lambda 15 15.0 0.0 Step Time Lambda 16 16.0 0.0 Step Time Lambda 17 17.0 0.0 Step Time Lambda 18 18.0 0.0 Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax 1000 Double precision normally gives you higher accuracy. You might need to increase your constraint accuracy, or turn off constraints alltogether (set constraints = none in mdp file) Why doesn't GROMACS output the energies for certain steps? Step 3 and steps 5-18 do show any output in the log file. Any ideas why this is happening? This happens for the reasons printed by mdrun - those steps caused no change in energy. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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 list gmx-users@gromacs.org
Re: [gmx-users] GROMACS/ORCA QMMM
Jose Tusell wrote: Hi Justin, Thanks for the input on why this is happening. It sounds a little suspicious that the energy doesn't change after a few steps of energy minimization. Do you know of any way that I can find out what is going on? The screen output should indicate the atom with maximal force. Sometimes the EM algorithms get stuck when the geometry cannot change without making detrimental moves. You either need a larger step size, a different algorithm, or a better starting structure, if that is the case. I have seen this many times before, nothing suspicious about it. -Justin Thanks, Jose Tusell On Thu, Nov 17, 2011 at 10:58 AM, Justin A. Lemkul jalem...@vt.edu wrote: Jose Tusell wrote: Hi Cristoph, Thanks for the reply. I found that my problem was not gromacs. The input that ORCA was receiving from GROMACS did not have the correct number of hydrogens. I've solved this problem now and ORCA is running fine. I however ran into another problem with my energy minimization. The output from my gromacs log file is the following: Step Time Lambda 00.00.0 Energies (kJ/mol) Bond AngleProper Dih. Improper Dih. LJ-14 1.21899e+041.92496e+035.62567e+031.49141e+013.68001e+03 Coulomb-14LJ (SR) Coulomb (SR) Coul. recip.Quantum En. 2.41200e+041.47494e+05 -5.06544e+05 -7.56009e+04 -3.96508e+06 Potential Pressure (bar) -4.35218e+06 -2.10629e+04 Step Time Lambda 11.00.0 Energies (kJ/mol) Bond AngleProper Dih. Improper Dih. LJ-14 1.20006e+041.92297e+035.62600e+031.47801e+013.67746e+03 Coulomb-14LJ (SR) Coulomb (SR) Coul. recip.Quantum En. 2.41174e+041.46421e+05 -5.06609e+05 -7.56156e+04 -4.00402e+06 Potential Pressure (bar) -4.39246e+06 -2.10739e+04 Step Time Lambda 22.00.0 Energies (kJ/mol) Bond AngleProper Dih. Improper Dih. LJ-14 1.17961e+041.92126e+035.62633e+031.46477e+013.67461e+03 Coulomb-14LJ (SR) Coulomb (SR) Coul. recip.Quantum En. 2.41145e+041.45528e+05 -5.06679e+05 -7.56315e+04 -4.18671e+06 Potential Pressure (bar) -4.57635e+06 -2.10854e+04 Step Time Lambda 33.00.0 Step Time Lambda 44.00.0 Energies (kJ/mol) Bond AngleProper Dih. Improper Dih. LJ-14 1.16705e+041.92041e+035.62652e+031.45728e+013.67282e+03 Coulomb-14LJ (SR) Coulomb (SR) Coul. recip.Quantum En. 2.41128e+041.45113e+05 -5.06721e+05 -7.56410e+04 -4.24486e+06 Potential Pressure (bar) -4.63509e+06 -2.10913e+04 Step Time Lambda 55.00.0 Step Time Lambda 66.00.0 Step Time Lambda 77.00.0 Step Time Lambda 88.00.0 Step Time Lambda 99.00.0 Step Time Lambda 10 10.00.0 Step Time Lambda 11 11.00.0 Step Time Lambda 12 12.00.0 Step Time Lambda 13 13.00.0 Step Time Lambda 14 14.00.0 Step Time Lambda 15 15.00.0 Step Time Lambda 16 16.00.0 Step Time Lambda 17 17.00.0 Step Time Lambda 18 18.00.0 Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax 1000 Double precision normally gives you higher accuracy. You might need to increase your constraint accuracy, or turn off constraints alltogether (set constraints = none in mdp file) Why doesn't GROMACS output the energies for certain steps? Step 3 and steps 5-18 do show any output in the log file. Any ideas why this is happening? This happens for the reasons printed by mdrun - those steps caused no change in energy. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar
[gmx-users] what's the math algorithm?
Dear all, Assuming I have a some tabulated potentials, table.xvg, tablep.xvg, table_P_P.xvg, table_P_C.xvg and so on. Also there are non-zero values in the first column of both table.xvg and tablep.xvg; while the first column (x), the six column (h(x)) and the last column (h'(x)) have non-zero numbers. All other columns have only 0. So what's the math behind it? Thanks. -- Best, Liang Liu -- 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] query for energy minimization in solvent
Yes I m using 4.0.7 version.so for that how could I change the name accordingly. On Sat, Nov 5, 2011 at 1:37 AM, Justin A. Lemkul jalem...@vt.edu wrote: Anushree Tripathi wrote: when i run the given command i.e, grompp -f minim.mdp -c 1AKI_solv_ions.gro -p topol.top -o em.tpr It is showing fatal error:No such molecule type NA. How could I troubleshoot this problem? Ion naming is listed in ions.itp - the NA name works for all force fields in the Gromacs 4.5.x series. Older versions had force field-specific naming so you will have to change the name accordingly if you're using one of these versions. -Justin -- ==**== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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] GROMACS/ORCA QMMM
I'll try changing the step size first and if that fails I'll try another algorithm. Thanks for the input. Jose Tusell On Thu, Nov 17, 2011 at 11:48 AM, Justin A. Lemkul jalem...@vt.edu wrote: Jose Tusell wrote: Hi Justin, Thanks for the input on why this is happening. It sounds a little suspicious that the energy doesn't change after a few steps of energy minimization. Do you know of any way that I can find out what is going on? The screen output should indicate the atom with maximal force. Sometimes the EM algorithms get stuck when the geometry cannot change without making detrimental moves. You either need a larger step size, a different algorithm, or a better starting structure, if that is the case. I have seen this many times before, nothing suspicious about it. -Justin Thanks, Jose Tusell On Thu, Nov 17, 2011 at 10:58 AM, Justin A. Lemkul jalem...@vt.edu wrote: Jose Tusell wrote: Hi Cristoph, Thanks for the reply. I found that my problem was not gromacs. The input that ORCA was receiving from GROMACS did not have the correct number of hydrogens. I've solved this problem now and ORCA is running fine. I however ran into another problem with my energy minimization. The output from my gromacs log file is the following: Step Time Lambda 0 0.0 0.0 Energies (kJ/mol) Bond Angle Proper Dih. Improper Dih. LJ-14 1.21899e+04 1.92496e+03 5.62567e+03 1.49141e+01 3.68001e+03 Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip. Quantum En. 2.41200e+04 1.47494e+05 -5.06544e+05 -7.56009e+04 -3.96508e+06 Potential Pressure (bar) -4.35218e+06 -2.10629e+04 Step Time Lambda 1 1.0 0.0 Energies (kJ/mol) Bond Angle Proper Dih. Improper Dih. LJ-14 1.20006e+04 1.92297e+03 5.62600e+03 1.47801e+01 3.67746e+03 Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip. Quantum En. 2.41174e+04 1.46421e+05 -5.06609e+05 -7.56156e+04 -4.00402e+06 Potential Pressure (bar) -4.39246e+06 -2.10739e+04 Step Time Lambda 2 2.0 0.0 Energies (kJ/mol) Bond Angle Proper Dih. Improper Dih. LJ-14 1.17961e+04 1.92126e+03 5.62633e+03 1.46477e+01 3.67461e+03 Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip. Quantum En. 2.41145e+04 1.45528e+05 -5.06679e+05 -7.56315e+04 -4.18671e+06 Potential Pressure (bar) -4.57635e+06 -2.10854e+04 Step Time Lambda 3 3.0 0.0 Step Time Lambda 4 4.0 0.0 Energies (kJ/mol) Bond Angle Proper Dih. Improper Dih. LJ-14 1.16705e+04 1.92041e+03 5.62652e+03 1.45728e+01 3.67282e+03 Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip. Quantum En. 2.41128e+04 1.45113e+05 -5.06721e+05 -7.56410e+04 -4.24486e+06 Potential Pressure (bar) -4.63509e+06 -2.10913e+04 Step Time Lambda 5 5.0 0.0 Step Time Lambda 6 6.0 0.0 Step Time Lambda 7 7.0 0.0 Step Time Lambda 8 8.0 0.0 Step Time Lambda 9 9.0 0.0 Step Time Lambda 10 10.0 0.0 Step Time Lambda 11 11.0 0.0 Step Time Lambda 12 12.0 0.0 Step Time Lambda 13 13.0 0.0 Step Time Lambda 14 14.0 0.0 Step Time Lambda 15 15.0 0.0 Step Time Lambda 16 16.0 0.0 Step Time Lambda 17 17.0 0.0 Step Time Lambda 18 18.0 0.0 Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax 1000 Double precision normally gives you higher accuracy. You might need to increase your constraint accuracy, or turn off constraints alltogether (set constraints = none in mdp file) Why doesn't GROMACS output the energies for certain steps? Step 3 and steps 5-18 do show any output in the log file. Any ideas why this is happening? This happens for
Re: [gmx-users] GROMACS/ORCA QMMM
hello, I am trying to simulate streptavidin tetramer-biotin complex.I ve calculated Ligand topology from a sofware PRODRG using gromos87 force fields.After solvating it,I am getting an error using grompp command Fatal error: Atomtype HW not found can anyone provide me some help? Thanx with anticipation. On Fri, Nov 18, 2011 at 2:29 AM, Jose Tusell jrta1...@gmail.com wrote: I'll try changing the step size first and if that fails I'll try another algorithm. Thanks for the input. Jose Tusell On Thu, Nov 17, 2011 at 11:48 AM, Justin A. Lemkul jalem...@vt.edu wrote: Jose Tusell wrote: Hi Justin, Thanks for the input on why this is happening. It sounds a little suspicious that the energy doesn't change after a few steps of energy minimization. Do you know of any way that I can find out what is going on? The screen output should indicate the atom with maximal force. Sometimes the EM algorithms get stuck when the geometry cannot change without making detrimental moves. You either need a larger step size, a different algorithm, or a better starting structure, if that is the case. I have seen this many times before, nothing suspicious about it. -Justin Thanks, Jose Tusell On Thu, Nov 17, 2011 at 10:58 AM, Justin A. Lemkul jalem...@vt.edu wrote: Jose Tusell wrote: Hi Cristoph, Thanks for the reply. I found that my problem was not gromacs. The input that ORCA was receiving from GROMACS did not have the correct number of hydrogens. I've solved this problem now and ORCA is running fine. I however ran into another problem with my energy minimization. The output from my gromacs log file is the following: Step Time Lambda 00.00.0 Energies (kJ/mol) Bond AngleProper Dih. Improper Dih. LJ-14 1.21899e+041.92496e+035.62567e+031.49141e+01 3.68001e+03 Coulomb-14LJ (SR) Coulomb (SR) Coul. recip.Quantum En. 2.41200e+041.47494e+05 -5.06544e+05 -7.56009e+04 -3.96508e+06 Potential Pressure (bar) -4.35218e+06 -2.10629e+04 Step Time Lambda 11.00.0 Energies (kJ/mol) Bond AngleProper Dih. Improper Dih. LJ-14 1.20006e+041.92297e+035.62600e+031.47801e+01 3.67746e+03 Coulomb-14LJ (SR) Coulomb (SR) Coul. recip.Quantum En. 2.41174e+041.46421e+05 -5.06609e+05 -7.56156e+04 -4.00402e+06 Potential Pressure (bar) -4.39246e+06 -2.10739e+04 Step Time Lambda 22.00.0 Energies (kJ/mol) Bond AngleProper Dih. Improper Dih. LJ-14 1.17961e+041.92126e+035.62633e+031.46477e+01 3.67461e+03 Coulomb-14LJ (SR) Coulomb (SR) Coul. recip.Quantum En. 2.41145e+041.45528e+05 -5.06679e+05 -7.56315e+04 -4.18671e+06 Potential Pressure (bar) -4.57635e+06 -2.10854e+04 Step Time Lambda 33.00.0 Step Time Lambda 44.00.0 Energies (kJ/mol) Bond AngleProper Dih. Improper Dih. LJ-14 1.16705e+041.92041e+035.62652e+031.45728e+01 3.67282e+03 Coulomb-14LJ (SR) Coulomb (SR) Coul. recip.Quantum En. 2.41128e+041.45113e+05 -5.06721e+05 -7.56410e+04 -4.24486e+06 Potential Pressure (bar) -4.63509e+06 -2.10913e+04 Step Time Lambda 55.00.0 Step Time Lambda 66.00.0 Step Time Lambda 77.00.0 Step Time Lambda 88.00.0 Step Time Lambda 99.00.0 Step Time Lambda 10 10.00.0 Step Time Lambda 11 11.00.0 Step Time Lambda 12 12.00.0 Step Time Lambda 13 13.00.0 Step Time Lambda 14 14.00.0 Step Time Lambda 15 15.00.0 Step Time Lambda 16 16.00.0 Step Time Lambda 17 17.00.0 Step Time Lambda
[gmx-users] non-specific protein-protein interactions
Dear gromacs list, Does anyone know how well current force fields capture the energetics of non-specific protein-protein interactions? I'm simulating a protein with an arm that alternates between (apparently) non-specific adsorption to the main-body of the protein and free movement in the solvent. Can I place any trust in the results of an MD simulation for something like this? I haven't seen any comparison of experimental results with simulation results of the energetics of non-specific protein-protein interactions so I'm a little skeptical about it. Currently I'm using generalized born implicit solvent, which is perhaps a mistake when solvation energies could be critical to the results. Cheers, Ben -- 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] Poor exchange probability for REMD
Dear GMX users， Recently i am performing the REMD simulation with Gromacs program and the temperature distribution for each replica was predicted with the server http://folding.bmc.uu.se/remd/;. However, after a 2-ns short test simulation with 64 replicas , i checked the exchange probability for the neighboring replicas and find the exchange probability was about 0.3 to 0.4 (as the file i attached )but the desired probability was 0.2. Meanwhile, i found the exchange probabilities fluctuated markedly for each pair of replicas while ideally we may hope they were consistent with each other. I don't know whether this is acceptable or must be fixed up, or a longer simulation time and pre-equilibrium at different replica temperature for each replica was needed. The system i simulated includes 60074 atoms which consists of 155 residues,19173 waters and 14 chloridions. I first equilibrium the system for 2ns with NPT ensemble at 300K, then start the REMD simulation for 64 different replicas (temperature ranges from 300 to 386K) with NVT ensemble and the exchange attempt time was 2-ps(1000 integral steps). Now i was totally puzzled and don't know how to figure out these problems,i am eager for the help from you and any suggestions will be greatly appreciated! Best regards! Xiangqian Kong -- 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] Hydrogen database
Most of the issues should wash out after energy minimization anyway, so I wouldn't care about bond angles too much. Just remember: the topology controls the geometry not the hydrogen database. Yes the hdb file format isn't too intuitive but after awhile I figured it out. Here some examples of hydrogens connected to SP and SP3 hybridized heavy atoms. I parameterize saturated hydrocarbon backbones a lot, so here is an example of 1-heptanol (HPOH): Atom Assignments (from the rtp entry): H72H31 H21 H12 | || | H71--C7--..--C3--C2--C1-H11 | || | H73H32 H22 O1-HO1 HDB entry: HPOH 8 1 2 HO1 O1 C1 H11 2 6 H1 C1 C2 O1 2 6 H2 C2 C3 C1 2 6 H3 C3 C4 C2 2 6 H4 C4 C5 C3 2 6 H5 C5 C6 C4 2 6 H6 C6 C7 C5 3 4 H7 C7 C1 O1 Here is isopentyl acetate (isoamyl acetate) (3-methyl-1-butyl-ethanoate) (IPAC): Atom Assignments (from the rtp entry): H12 | H11-C1-H13 | C=O / OM \ H21-C2-H22 | H31-C3-H32 | C4-H41 / \ / \ H411-C41 C42-H423 / | | \ H412 H413 H421 H422 HDB entry: IPAC 6 3 4 H1 C1 C O 2 6 H2 C2 C3 OM 2 6 H3 C3 C4 C2 1 2 H41 C4 C41 C3 3 4 H41 C41 C4 C3 3 4 H42 C42 C4 C3 On 2011-11-17 10:11:52AM -0600, Ehud Schreiber wrote: Hi, I have recently studied the hydrogen database format of .hdb files (page 118, section 5.6.4 in the manual version 4.5.4). I would like to make a few remarks that, if correct, may need addressing. 1) Method 3 of adding the hydrogens, that of two planar hydrogens, gives -NH2 as the example. I think this is misleading, as although this is true for an amide group –C(=O)NH2 such as in an asparagine and glutamine side chains, the nitrogen is tetrahedral in the R-NH2 case or in the amino acid N-terminus. A better example for two planar hydrogens would be =CH2 such as in ethylene or vinyls. 2) The provided methods for adding hydrogens are not covering the whole set of possibilities. In particular, it seems to me that three methods are lacking, although admittedly they are less common: a. One tetrahedral hydrogen connected to atom i which is in turn connected to two atoms j,k such that n is on the plane bisecting angle j-i-k; n-i-j = n-i-k = 109.47 degrees; and dihedral n-i-j-l 90 degrees. Example: secondary amines R2NH. This case can be mimicked by method 2 with i,j,l atoms so is perhaps superfluous. b. One planar hydrogen connected to atom i which is connected to only one other atom j such that n-i-j = 120 degrees and n-i-j-k is trans. Example: R2C=NH. c. One linear hydrogen such that n-i-j is a straight line. Example: #CH where # is a triple bond. 3) I haven’t checked this, but can the k atom be a hydrogen added in an earlier line of the same .hdb file? What do you say? Thanks, Ehud Schreiber. -- 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 -- == Peter C. Lai| University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu| Birmingham AL 35294-4461 (205) 690-0808 | == -- 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] analysing helix dynamics
Hi all, During MD simulations of a protein,I find that there are two helices switch periodically from being parallel and perpendicular to each other. I'd like to plot out the orientation of these two helices with respect to each other, is there a command to extract this information? JJ http://www.chick.com/reading/tracts/1071/1071_01.asp -- 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] fatal occur occuring
hello, I am trying to simulate streptavidin tetramer-biotin complex.I ve calculated Ligand topology from a sofware PRODRG using gromos87 force fields.After solvating it,I am getting an error using grompp command Fatal error: Atomtype HW not found can anyone provide me some help? Thanx with anticipation. -- 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] fatal occur occuring
swati patel wrote: hello, I am trying to simulate streptavidin tetramer-biotin complex.I ve calculated Ligand topology from a sofware PRODRG using gromos87 force fields.After solvating it,I am getting an error using grompp command Fatal error: Atomtype HW not found can anyone provide me some help? The HW type is specific for the Gromos87 force field (i.e. gmx.ff in Gromacs), so if you're getting this fatal error, you're somehow mixing and matching force fields, likely between Gromos87 and Gromos96. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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] difference in force fields.
swati patel wrote: helo justin, yess since i am dealing with a complex,so i generated protein topology using gromos96 43a1 force fields and for ligands,obtained topology using PRODRG which uses gromos 87 force fields. How to obtain similar force fields topologies since PRODRG only works with gromos87 force fields and in gromacs i choosed optipn (9)i.e.gromos 96 force fields.?? This is not true. There is a newer PRODRG server that creates topologies for Gromos96. Their quality is not particularly high, as noted on this list on a weekly basis, and in the literature. Please see the paper linked from: http://www.gromacs.org/Downloads/Related_Software/PRODRG#Tips -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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] PRODRG2.5 server not found.
Helo Justin, The link for prodrg 2.5 server is i.e. http://davapc1.bioch.dundee.ac.uk/cgi-bin/prodrg_beta is 404 not found.How should I proceed further? Thanx. -- 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] problem obtaining similar force fields for protein and ligand
Hello Users, I am facing a problem in obtaining topologies for my ligand.I tried working on acpype,bt it seems very complex to me.PRODRG is easy but it uses gromos87 force field.PRODRG 2.5 is still not available for download. can anyone suggest me how to obtain topologies for my protein and ligand using same force fields? thanks. -- 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] Regarding cosine content
Thanks for the reply... I calculated principal components per protein using the command g_anaeig -f md.xtc -s md.tpr -v eigenvec.trr -eig eigenval.xvg -comp eigcomp.xvg -rmsf eigrmsf.xvg -2d 2dproj.xvg -proj proj.xvg -tu ns -extr extr.pdb -filt filt.xtc -first 1 -last 2 Also please suggest how one can differentiate between the two scenarios, when the high cosine content is due to random diffusion or conformational changes ? On Thu, Nov 17, 2011 at 17:34, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Bipin, It seems one of the proteins is taking longer to reach an equilibrium. Maybe it is undergoing a conformational change? Did you calculate the principal components per protein, or for the joint trajectories? It would have been better to echo the commands you used on the list, because it might result in a different interpretation. I also made some comments on the list a short while ago regarding the interpretation of projections and cosine content. Maybe they can help you form a picture of what is happening :) Hope it helps, Tsjerk On Thu, Nov 17, 2011 at 12:22 PM, bipin singh bipinel...@gmail.com wrote: Hello all, I have done PCA from 50ns long trajectory for two similar proteins (length 180 aa and RMSD 0.2 A). The equilibration time and final simulation condition were identical for both the protein. But when I checked the cosine content for PC1 for both proteins they were 0.9 and 0.5 respectively. What can be the reason for this huge difference in cosine content of the two proteins ? -- --- Regards, Bipin Singh -- gmx-users mailing list gmx-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 -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- gmx-users mailing list gmx-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 -- --- Regards, Bipin Singh -- --- Regards, Bipin Singh -- 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
