[gmx-users] About Compiler Compatibility for Gromacs 4.6.2 Compilation
Dear Justin and Mark Thank you for your Previous reply Can i Use the Following Intel Compiler for grmacs 4.6.2 in centos Linux OS ? Intel® C++ Composer XE 2013 for Linux it Includes Intel® C++ Compiler, Intel® Integrated Performance Primitives 7.1, Intel® Math Kernel Library 11.0, Intel Cilk™ Plus, the Intel® Threading Building Blocks (Intel® TBB)” -- 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] Reg error in Compilation Of Gromacs 4.6.2
Dear Justin Thank you for your Previous reply, I am trying to Install gromacs 4.6.2 in a cluster having centos OS with teh Following Command I got following error cmake .. -DGMX_BUILD_OWN_FFTW=ON -DGMX_MPI=ON -DGMX_DOUBLE=ON CMake Warning at CMakeLists.txt:785 (message): No C AVX flag found. Consider a newer compiler, or try SSE4.1 (lower performance). CMake Warning at CMakeLists.txt:802 (message): No C FMA4 flag found. Consider a newer compiler, or try SSE4.1 (lower performance). CMake Error at CMakeLists.txt:872 (gmx_test_avx_gcc_maskload_bug): GMX_TEST_AVX_GCC_MASKLOAD_BUG Macro invoked with incorrect arguments for macro named: GMX_TEST_AVX_GCC_MASKLOAD_BUG -- The GROMACS-managed build of FFTW 3 will configure with the following optimizations: --enable-sse2 -- Configuring incomplete, errors occurred! The Aforesaid Error Indicates What is the Lack ? I Think I need Latest Compiler (Please Indicate Version) is it Correct Not? How to solve the problem What are Prerequestite i need ? Already Gromacs 4.5.5 has been installed sucessfully 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
[gmx-users] reg GPU Mdrun Error
respected mark sir , Thank you fro your previous reply When i run the production Mdrun I have got the following error job is terminating with segmentation fault error Back Off! I just backed up CNTPEPRSOLIONSfullplumedGPUtest2.log to ./#CNTPEPRSOLIONSfullplumedGPUtest2.log.5# Reading file CNTPEPRSOLIONSfullGPUtest2.tpr, VERSION 4.6.1 (single precision) Using 3 MPI threads Using 5 OpenMP threads per tMPI thread 3 GPUs detected: #0: NVIDIA Tesla K20m, compute cap.: 3.5, ECC: no, stat: compatible #1: NVIDIA Tesla K20m, compute cap.: 3.5, ECC: no, stat: compatible #2: NVIDIA Tesla K20m, compute cap.: 3.5, ECC: no, stat: compatible 3 GPUs auto-selected for this run: #0, #1, #2 NOTE: The number of threads is not equal to the number of (logical) cores and the -pin option is set to auto: will not pin thread to cores. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). Back Off! I just backed up CNTPEPRSOLIONSfullplumedGPUtest2.trr to ./#CNTPEPRSOLIONSfullplumedGPUtest2.trr.5# Back Off! I just backed up CNTPEPRSOLIONSfullplumedGPUtest2.edr to ./#CNTPEPRSOLIONSfullplumedGPUtest2.edr.5# WARNING: This run will generate roughly 27348 Mb of data starting mdrun 'C225N99O45 in water' 1000 steps, 2.0 ps. Segmentation fault (core dumped) What is the meaning of the note ? How to Give the command to run? i gave as follows mdrun -s CNTPEPRSOLIONSfullplumed.tpr -plumed plumed1.dat -nb gpu -v -deffnm CNTPEPRSOLIONSfull -cpt 2 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
[gmx-users] Reg Mpi run Error
Dear Jutin and Marks Thnak you for your previous reply Whrn i run the following job in cluster as follows [hinditron@compute002 gromacs-plumed-cpu-input]$ mpirun -np 8 -machinefile ~/myhosts mdrun_mpi -s CNTPEPRSOLIONSfullcputest.tpr -v -deffnm CNTPEPRSOLIONSfull -cpt 2 I have eceived the error as follows Sisters Have Always Fascinated Me (Speech) Error on node 3, will try to stop all the nodes Halting parallel program mdrun_mpi on CPU 3 out of 8 Halting parallel program mdrun_mpi on CPU 4 out of 8 gcq#33: Sisters Have Always Fascinated Me (Speech) [cli_6]: aborting job: application called MPI_Abort(MPI_COMM_WORLD, -1) - process 6 gcq#33: Sisters Have Always Fascinated Me (Speech) gcq#33: Sisters Have Always Fascinated Me (Speech) [cli_3]: aborting job: application called MPI_Abort(MPI_COMM_WORLD, -1) - process 3 [cli_2]: gcq#33: Sisters Have Always Fascinated Me (Speech) [cli_5]: aborting job: application called MPI_Abort(MPI_COMM_WORLD, -1) - process 5 aborting job: application called MPI_Abort(MPI_COMM_WORLD, -1) - process 2 gcq#33: Sisters Have Always Fascinated Me (Speech) [cli_4]: aborting job: application called MPI_Abort(MPI_COMM_WORLD, -1) - process 4 === = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES = EXIT CODE: 65280 = CLEANING UP REMAINING PROCESSES = YOU CAN IGNORE THE BELOW CLEANUP MESSAGES what is the meaning of above error How to solve it? 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
[gmx-users] Reg mpirun error
Thank you justin for your reply The error I have pasted here (also pasted in previous mail) is total screen ouptut. No further output as you stated in previous mail( The real error is further up in the screen output or in the .log file.) [hinditron@compute002 gromacs-plumed-cpu-input]$ mpirun -np 8 -machinefile ~/myhosts mdrun_mpi -s CNTPEPRSOLIONSfullcputest.tpr -v -deffnm CNTPEPRSOLIONSfull -cpt 2 I have eceived the error as follows Sisters Have Always Fascinated Me (Speech) Error on node 3, will try to stop all the nodes Halting parallel program mdrun_mpi on CPU 3 out of 8 Halting parallel program mdrun_mpi on CPU 4 out of 8 gcq#33: Sisters Have Always Fascinated Me (Speech) [cli_6]: aborting job: application called MPI_Abort(MPI_COMM_WORLD, -1) - process 6 gcq#33: Sisters Have Always Fascinated Me (Speech) gcq#33: Sisters Have Always Fascinated Me (Speech) [cli_3]: aborting job: application called MPI_Abort(MPI_COMM_WORLD, -1) - process 3 [cli_2]: gcq#33: Sisters Have Always Fascinated Me (Speech) [cli_5]: aborting job: application called MPI_Abort(MPI_COMM_WORLD, -1) - process 5 aborting job: application called MPI_Abort(MPI_COMM_WORLD, -1) - process 2 gcq#33: Sisters Have Always Fascinated Me (Speech) [cli_4]: aborting job: application called MPI_Abort(MPI_COMM_WORLD, -1) - process 4 === = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES = EXIT CODE: 65280 = CLEANING UP REMAINING PROCESSES = YOU CAN IGNORE THE BELOW CLEANUP MESSAGES you Mailed me this is generic mpirun error (These are generic mpirun failure messages) But No error message shown in .log file Could you please help to solve this error? With Regards S.Vidhyasankar -- 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] About script for free energy calculation
Dear Justin thank you for your Previous reply I am following your methane/water free energy tutorial I have Generated All .mdp files wiht Different LAMBDA value But When I Run job using Your Job.sh script in usr/local/gromacs4.6.2/bin I have Received the Following error ( I ma running this script by keepig in BIN directory) root@vidhyasankar-desktop:/usr/local/gromacs4.6.1/bin# ./job.sh ( the error is as follows) Free energy home directory set to /usr/local/gromacs4.6.1/bin/Free_Energy .mdp files are stored in /usr/local/gromacs4.6.1/bin/Free_Energy/MDP Starting minimization for lambda = 0... ./job.sh: line 28: grompp_d: command not found ./job.sh: line 30: mdrun_d: command not found ./job.sh: line 41: grompp_d: command not found ./job.sh: line 45: mdrun_d: command not found Minimization complete. Starting constant volume equilibration... ./job.sh: line 60: grompp_d: command not found ./job.sh: line 62: mdrun_d: command not found Constant volume equilibration complete. Starting constant pressure equilibration... ./job.sh: line 77: grompp_d: command not found ./job.sh: line 79: mdrun_d: command not found Constant pressure equilibration complete. Starting production MD simulation... ./job.sh: line 93: grompp_d: command not found ./job.sh: line 95: mdrun_d: command not found Production MD complete. Ending. Job completed for lambda = 0 How to Solve it Thanks InAdvance -- 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] About Error in mdrun
Dear justin Thank you for your previous reply When i run the md in gromacs 4.6.2 with plumed1.3 Plugin i have got the error as follows The number of threads is not equal to the number of (logical) cores and the -pin option is set to auto: will not pin thread to cores. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). Back Off! I just backed up CNTPEPRSOLIONSfull.trr to ./#CNTPEPRSOLIONSfull.trr.3# Back Off! I just backed up CNTPEPRSOLIONSfull.edr to ./#CNTPEPRSOLIONSfull.edr.3# WARNING: This run will generate roughly 273370 Mb of data starting mdrun 'C225N99O45 in water' 1 steps, 20.0 ps. ! PLUMED ERROR: PluMed dead with errors: check log file ! ABORTING RUN Segmentation fault (core dumped) To avoid this May i use -pin on ? Thnaks 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
[gmx-users] About running Production simulation in GPU with twinrange cut-off
Thank you Justin To check Performance in GPU i Need to run simulation with same parameters for r coulomb = rvdw rlist = 0.9 ; short-range neighborlist cutoff (in nm) rcoulomb = 1.4 ; short-range electrostatic cutoff (in nm) rvdw = 1.4 But i need to use twin range interaction with rvdw = 1.4; r coulomb = 0.9 in GPU May i use different option -nb or -tunepme option of mdrun instead -testverlet But in one mail to me you said that the defaut parameters for Gromos96 53A6, nstlist = 5 rlist = 0.9 rcoulomb = 0.9 rvdw = 1.4 but if i run on GPU regularly i need to change rcoulomb = 1.4 from 0.9 Will it Affect the result ? or is it reasonable to change ? 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
[gmx-users] About Running production simualtion in GPU
Thank you Justin for your pervious reply As you mailed me When using PME, the rcoulomb is little bit fiexible and Validationof Modification is necessary . But How to Validate Such Modification ? i request you Humbly to give Little bit claear idea . Also What is the Procedure to Do Validation.? Thanks In Advance With Regards S.Vidhyasankar -- 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] About running gromacs in GPU
Dear Justin Thank you for your previoue reply I have prepared a .tpr file to run it run Successfully in CPU But when i use the Same .tpr files to run in GPU , It have not run successfully What is reason ? What Command Should I give When I run .tpr file in GPU I Hope it may be mdrun -s input.tpr -testverlet Should i add any more flag ? Also I have different rvdw and Coulomb Cut-offs rlist = 0.9 rcoulomb = 0.9 rvdw = 1.4 The following is error Message The VdW and Coulomb cut-offs are different, whereas the Verlet scheme only supports equal cut-offs For more information and tips for troubleshooting, please check the GROMACS 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
[gmx-users] About Physical parameters
Dear Justin Thank you for your Previuos reply I am using gromos53a6 ff When i changed the parameters for cut-off (r list ) value to 1.2 I have got Error as follows What is the Meaning of Note 2 3 NOTE 2 [file cntcycpepfull2.mdp]: The switch/shift interaction settings are just for compatibility; you will get betterperformance from applying potential modifiers to your interactions! NOTE 3 [file cntcycpepfull2.mdp]: For energy conservation with switch/shift potentials, rlist should be 0.1 to 0.3 nm larger than rcoulomb. NOTE 4 [file cntcycpepfull2.mdp]: For energy conservation with switch/shift potentials, rlist should be 0.1 to 0.3 nm larger than rvdw. WARNING 1 [file cntcycpepfull2.mdp]: The sum of the two largest charge group radii (0.518710) is larger than rlist (1.20) - rvdw (1.20) WARNING 2 [file cntcycpepfull2.mdp]: The sum of the two largest charge group radii (0.518710) is larger than rlist (1.20) - rcoulomb (1.20) nstlist= 5 rlist= 1.2 rcoulomb= 1.2 vdwtype = Shift rvdw= 1.2 coulombtype= Reaction-Field-zero pme_order= 4 fourierspacing= 0.16 pcoupl= Parrinello-Rahman pcoupltype= isotropic thus .grompp terminated due to warnings To Avoid his I have used the rlist=1.8 (in Above valuue) Because the difference betwen rlist-rcoloum should Be greater than 0.518710 But you maild me the cut-off looks Bizarre .it should be based on parent force field(mine is gromos53a6) I hope your kind Suugestion are useful to get succesfull production mdrun 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
[gmx-users] About coulmb Vanderrwalls cutoff
Dear Justin Thank you for yoyr Previuos reply I am using Gromos96 53a6 so i am using the following parameters ns_type = grid nstlist = 5 rlist = 0.9 rcoulomb = 0.9 rvdw = 1.4 is this value is reasonable ? But when i run the grommp i got warnings as follows nstcomm nstcalcenergy defeats the purpose of nstcalcenergy, setting nstcomm to nstcalcenergy NOTE 2 [file CNTPEPnvt.mdp]: You are using a cut-off for VdW interactions with NVE, for good energy conservation use vdwtype = Shift (possibly with DispCorr) NOTE 3 [file CNTPEPnvt.mdp]: You are using a cut-off for electrostatics with NVE, for good energy conservation use coulombtype = PME-Switch or Reaction-Field-zero if Chnge vdwtupe=shift with disspCorr = DispCorr = EnerPres I have got the error as follows WARNING 2 [file CNTPEPnvt.mdp]: The sum of the two largest charge group radii (0.498722) is larger than rlist (0.90) - rvdw (1.40) How to to Avoid this error? (Due to warning grompp_d terminated ) 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
[gmx-users] About coulmb Vanderrwalls cutoff
Dear Justin Thank you for your Previous reply. As yo mailed me The Defaut Value for vandewalls and Electrostatics in GROMOS96 53A6 is PME option s_type = grid nstlist = 5 rlist = 0.9 rcoulomb = 0.9 rvdw = 1.4 But in you Umbrella sampling you are using GROMOS96 53A6 FF there you quoted different Parameters in your em.mdp file nstlist = 1 ; Frequency to update the neighbor list and long range forces ns_type = grid ; Method to determine neighbor list (simple, grid) rlist = 1.4 ; Cut-off for making neighbor list (short range forces) coulombtype = PME ; Treatment of long range electrostatic interactions rcoulomb= 1.4 ; Short-range electrostatic cut-off rvdw= 1.4 ; Short-range Van der Waals cut-off pbc = xyz can i Take 1.4 instead of 0.9 value oterwise is there is Any spcification according to system and BOx size Thanks Inadvance -- 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] About coulmb Vanderrwalls cutoff
Dear Justin thank you for your previous reply How can i check using th value 1.4 is harmless to My system Through g_energy ouput (potential.xvg) can i check (graphically) Thnaks 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
[gmx-users] About Concatenation of several trajectory files
Dear Justin, Mark other gromacs users Thank you fro your previuos replies I need to concatenate several .trr , .xtc and .edr files . Is there is any gromacs tools availble ? or Is it enough to use cat command in Linux 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
[gmx-users] Compilation error
Dear Gromacs user Thank you for your previous reply When i Compile gromacs 4.5.6 I have Gor following error collect2: ld returned 1 exit status make[3]: *** [grompp] Error 1 make[3]: Leaving directory `/root/gromacs-4.5.6/src/kernel' make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory `/root/gromacs-4.5.6/src' make[1]: *** [all] Error 2 make[1]: Leaving directory `/root/gromacs-4.5.6/src' make: *** [all-recursive] Error 1 I configure with Following Command ./configure --enable-double --with-fft=fftpack --program-suffix=_d I Have fftw3.3.2 but i have Not used that I am using the deh=fault fftpack How to Solve this error What went wrong? I am using gcc 4.6.3 in Ubunt12.04 OS already I have Successfully installed gromacs 4.6 it run well 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
[gmx-users] About Checkpoint error in gromacs 4.6
Dear Justin Thank you for your previuos reply I am using gromacs 4.6 AMD 8 core processor When I run restart My run from the Checkpoint file using the following error ./mdrun_d -s CNTPEPRSOLNPT.tpr -cpi CNTPEPRSOLNPT_prev.cpt -v -nt 8 -deffnm CNTPEPRSOLNPT -append The original run wrote a file called 'CNTPEPRSOLNPT.trr' which is larger than 2 GB, but mdrun did not support large file offsets. Can not append. Run mdrun with -noappend How to solve this error? Thnaks 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
[gmx-users] About Checkpoint error in gromacs 4.6
Respected Erik Marklund, Thank you for your reply When i run with a -noappend option from the checkpoint it runs well but Ooutput files are in Different Names The files Are not merged (are not Continues) ./mdrun_d -s CNTPEPRSOLNPT.tpr -cpi CNTPEPRSOLNPT_prev.cpt -v -nt 8 -deffnm CNTPEPRSOLNPT -noappend -- 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] About Checkpoint error in gromacs 4.6
Deat Justin Thank you for your Previuos Reply, But When I Run tne the following command with Append Option mdrun_d -s CNTPEPRSOLNPT.tpr -cpi CNTPEPRSOLNPT_prev.cpt -v -nt 8 -deffnm CNTPEPRSOLNPT -append I Have got the following error The original run wrote a file called 'CNTPEPRSOLNPT.trr' which is larger than 2 GB, but mdrun did not support large file offsets. Can not append. Run mdrun with -noappend How to Solve this ? But When i Run With -noappend option It run Well But it Produce different File Name files Are not merged (are not Continues) 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
[gmx-users] About Compiler Option
Dear Justin and other gromacs users , Thank you for your Previous reply I Have AMD Block Edition FX8350 Processor Also I have Ubuntu 10.04 OS Using 8 MPI threads Compiled acceleration: SSE4.1 (Gromacs could use AVX_128_FMA on this machine, which is better) As you mailed me for the aforesaid about performance I want to Ugrade gcc version 4.7.2 already i had version gcc 4.4.3 When I want to Upgrade But Though I give the following Commands add-apt-repository ppa:ubuntu-toolchain-r/test apt-get update apt-get install gcc-4.7 it has not been updated this is confirmed When i check gcc version in terminal -- 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] About Compilation error in gromacs 4.6
Dear Justin Thank you for your Previous reply, I have Downloaded gromacs 4.6 I have configured well using the following command cmake .. -DCMAKE_INSTALL_PREFIX=/usr/local/gromacs4.6 -DGMX_DOUBLE=ON -DGMX_BINARY_SUFFIX=_d and when i Compile using make command I have got following error make[2]: *** [src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_128_fma_double/nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_avx_128_fma_double.c.o] Error 1 make[1]: *** [src/gmxlib/CMakeFiles/gmx.dir/all] Error 2 make: *** [all] Error 2 How to solve the error What Dependencies should I install to solve This Error I Have installed gCC ,g++ compiler and fftw3.3 in My Ubuntu 10.04 OS I have AMD 8 core processor 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
[gmx-users] About Warnings in Mdrun
Thank you Mirco Wahab and Other Gromacs users As you Mailed Me I have compiled gromacs 4.6 I have installed using the command As posted in mail But I have AMD 8 Core black Edition When I run the mdrun I saw a warning Note: file tpx version 73, software tpx version 83 Using 8 MPI threads Compiled acceleration: SSE4.1 (Gromacs could use AVX_128_FMA on this machine, which is better) What is the Meaning of the Above statement ? How to raise the Performance -- 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] About CNT wrapped by Cyclic peptide
Dear Mark and Justin Thank you for yours previous Replies; You Mailed ME that My NVT and NPT equilibration is seems to be crashed . But Actually My NVT Equlibration and NPT Equlibation was Sucessfull It gives Nice output without Lincs warning , System exploding But My Question Is there is Any Relation between System size and Equilibration Time Because My I ran 2 ns equilibration (fro Both NPT NVT ) So I want to Increase the time step to atleast 10 ns 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
[gmx-users] About CNT cyclic PEptide
Dear Mark/justin Thank you for Previous reply My Final Production MD only shows Error Like Lincs , System Exploding And segmentation Fault TO Avoid this May I Further Extend My equilibration from 2 ns to 10 ns ? 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
[gmx-users] About Production MD run error
Dear Justin Thank you for previous reply. I am doing Carbon nano tubes Wrapped by Cyclic peptide .I am sure of that iher is no error in My topology of My system (CNT Wrapped by Cyclic peptide) After Successful NPT and NVT equilibration When i Run Production MD I have got The following Notes in terminal NOTE 1 [file CNTCYCfull.mdp]: nstcomm nstcalcenergy defeats the purpose of nstcalcenergy, setting nstcomm to nstcalcenergy NOTE 2 [file CNTCYCfull.mdp]: You are using a cut-off for VdW interactions with NVE, for good energy conservation use vdwtype = Shift (possibly with DispCorr) NOTE 3 [file CNTCYCfull.mdp]: You are using a cut-off for electrostatics with NVE, for good energy conservation use coulombtype = PME-Switch or Reaction-Field-zero NOTE 4 [file gfggZ.top, line 60]: For energy conservation with LINCS, lincs_iter should be 2 or larger. if I ignore the Notes I am Not Able to run . S I have Changed All options Accordingly in .mdp files Then When I run I have got the following errors after few Minutes step 100, will finish Thu Oct 10 18:44:32 2013 Step 153, time 0.0306 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.010047, max 0.158996 (between atoms 875 and 873) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length rms 37613.979597, max 954780.695847 (between atoms 1189 and 1190) 1157 1156 34.0 0.0997 0.1118 0.1000 bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 1171 1158 36.4 0.1542 0.1972 0.1530 1159 1158 34.8 0.1534 0.2022 0.1530 1178 1176 67.6 0.1528 2.4354 0.1530 1179 1177 79.1 0.1533 0.2981 0.1530 1046 1044 35.1 0.1489 0.3847 0.1470 Fatal error: 3 particles communicated to PME node 2 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension x. This usually means that your system is not well equilibrated. For more information and tips for troubleshooting, please check the GROMACS 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
[gmx-users] About Warnings and Note in Production MD
Dear Justin Thank you for previous reply. I am doing Carbon nano tubes Wrapped by Cyclic peptide After NPT and NVT equilibration When i Run Production MD I have got The following Notes in terminal NOTE 1 [file CNTCYCfull.mdp]: nstcomm nstcalcenergy defeats the purpose of nstcalcenergy, setting nstcomm to nstcalcenergy NOTE 2 [file CNTCYCfull.mdp]: You are using a cut-off for VdW interactions with NVE, for good energy conservation use vdwtype = Shift (possibly with DispCorr) NOTE 3 [file CNTCYCfull.mdp]: You are using a cut-off for electrostatics with NVE, for good energy conservation use coulombtype = PME-Switch or Reaction-Field-zero NOTE 4 [file gfggZ.top, line 60]: For energy conservation with LINCS, lincs_iter should be 2 or larger. if I ignore the Notes I am Not Able to run . S I have Changed All options Accordingly in .mdp files Then When I run I have got the following errors after few Minutes rms 37613.979597, max 954780.695847 (between atoms 1189 and 1190) 1157 1156 34.0 0.0997 0.1118 0.1000 bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 1171 1158 36.4 0.1542 0.1972 0.1530 1159 1158 34.8 0.1534 0.2022 0.1530 1178 1176 67.6 0.1528 2.4354 0.1530 1179 1177 79.1 0.1533 0.2981 0.1530 1046 1044 35.1 0.1489 0.3847 0.1470 step 141: Water molecule starting at atom 106721 can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. Wrote pdb files with previous and current coordinates Wrote pdb files with previous and current coordinates Segmentation fault So I Have reduced the Time step Again I have received the same error as follows but this time Wrote pdb files with previous and current coordinates Wrote pdb files with previous and current coordinates Segmentation fault How to Avoid Should I Equilibrate for Longer time? . I Have done 2ns Equilibration Only Is My equilibration is not enough? 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
[gmx-users] Notes from Production MD
Dear Baptiste , Thank you for your reply I have checked Nothing Wrong in the corresponding atom environments also if is Bad contacts During Energy Minimization it shows error .BUT My EM was successful . I Think Equilibration is not enough How to check Whether My system is attained equilibrium or Not ? 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
[gmx-users] About Merging topologies
Dear Justin thank you for your reply, Is there is Any tool to merge topology of CNT (generated by g_x2top tool) and Cyclic Peptide ( created by pdb2gmx) . otherwise Mere copy and Pasting the Corresponding Entries of CNT ( atom, Bond ,Angle, Dihedral Section) to topology of Cyclic peptide Also Should i Combine .RTP of CNT .RTP of Cyclic Peptide for My system (My system CNT wrapped By cyclic Peptide ) How to combine ? Mere Coy and Editing ( Changing Number and Oder) and put it .RTP data base Thanks in Advance S.Vidhyasankar -- 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] About Topology construction for CNT wrapped by Cyclic peptide
Dear Justin , Thank you for your reply, I need to construct Topology For Carbon Nano tubes (CNT) in gromoff53a5.ff . For that When i run the Following Command ./g_x2top_d -f CNT.gro -o CNT.top -r CNT.rtp I have got Error as follows Can not find forcefield for atom N-325 with 0 bonds Can not find forcefield for atom CA-326 with 2 bonds Can not find forcefield for atom CB-327 with 2 bonds Can not find forcefield for atom CG-328 with 2 bonds Can not find forcefield for atom C-330 with 2 bonds Can not find forcefield for atom O-331 with 1 bonds Can not find forcefield for atom N-332 with 0 bonds Can not find forcefield for atom C-836 with 3 bonds Can not find forcefield for atom C-837 with 3 bonds Can not find forcefield for atom C-838 with 2 bonds Can not find forcefield for atom C-839 with 2 bonds Can not find forcefield for atom C-840 with 3 bonds Can not find forcefield for atom C-841 with 3 bonds Can not find forcefield for atom C-842 with 2 bonds Can not find forcefield for atom C-843 with 2 bonds Could only find a forcefield type for 321 out of 843 atoms How to solve it ? 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
[gmx-users] About CNT-CYCLIC PETIDE constructio
Dear Justin Thank you for your Previous reply, I would Like to Construct a system of Single walled Carbon Nano tubes (SWCNT) Which should be Wrapped by Assembly of Cyclic Peptide . it Means CNT should be inserted Along the Cavity of Cyclic peptide I have separate .gro file for Both CNT and Assembly of Cyclic Peptide How to Merge These two .gro files As in the Aforesaid Manner. I hope your suggestion would He Helpful to me With Regards S.vidhyasankar -- 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] About Deutrium Order Parameter
Dear Justin Thank you for your Previous reply, I want to calculate Variation of deuterium order Parameter With respect to Time for Entire Trajectory and Hydration Number of Phosphate oxygen For My Entire Trajectory . Thereby I can Identify the Equilibration Time For My Membrane Is There is Any Tool in gromacs? 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
[gmx-users] About Detrium order Parameter
Dear Justin Thank you for your Previous Reply I am following you Protein Lipid Tutorial . In Analysis Part I Have Done Deuterium Order Parameters Analysis using index files . Kindly brief About Deuterium order parameter Analysis From the Graph How to interpret and Conclude Result ? 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
[gmx-users] About Check point for restart
Dear Justin Thank you for previous reply, There is power cut when i run My simulation So My System Gets Automatically restarted (Due to Low ups Power Packing) Then I want To restart My simulation using the obtained Checkpoint so i am using the following Command to restart ./mdrun_d -s emdppccycN31_solionsfull.tpr -cpi emdppccycN31_solionsfull_prev.cpt -v -nt 4 -deffnm emdppccycN31_solionsfull -cpt 2 -append But I have Got the following Error Checksum wrong for 'emdppccycN31_solionsfull.log'. The file has been replaced or its contents has been modified. Could you please suggest me a solution ? 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
[gmx-users] error in md.log files
Dear Justin Thank you for your reply, I have set the Restraint Along the Z Axis . as follows #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] i funct fcx fcy fcz 1 1 0 0 100 #endif Are you using the correct define statement in the .mdp file, and is your #ifdef in the correct location in the topology ? As you have Asked above in previous mail i have used the define = -DPOSRES -DPOSRES_WATER in my .mdp file My question is 1) Should i use -DPOSRES_WATER statement or Not in .mdp file ? Also I have used the #ifdef statement in the correct location in the topology as follows . ; Include water topology #include gromos53a6_lipid.ff/spc.itp #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcx fcy fcz 1 1 0 0 10 #endif ; Include topology for ions #include gromos53a6_lipid.ff/ions.itp 2) in My md.log files I have got following Lines At The end of Every 100 steps While it runs Smoothly Without Any Error . Large VCM(group NA): -0.01457, -0.01793, -0.03262, Temp-cm: inf Large VCM(group NA): -0.00894, -0.07417, -0.08968, Temp-cm: inf Large VCM(group NA): 0.00260, -0.05862, -0.10835, Temp-cm: inf Large VCM(group NA): 0.02240, 0.06127, -0.08617, Temp-cm: inf Large VCM(group NA): 0.11406, 0.11506, -0.07386, Temp-cm: inf Large VCM(group NA): 0.16859, 0.05669, -0.03958, Temp-cm: inf Large VCM(group NA): 0.07832, -0.04243, -0.02288, Temp-cm: inf Large VCM(group NA): -0.05293, -0.02293, -0.03210, Temp-cm: inf Large VCM(group NA): 0.01289, 0.09823, -0.02071, Temp-cm: inf Large VCM(group NA): 0.09863, 0.18033, 0.03704, Temp-cm: inf Large VCM(group NA): 0.01632, 0.22306, 0.04888, Temp-cm: inf Large VCM(group NA): -0.04317, 0.22376, -0.02476, Temp-cm: inf Large VCM(group NA): 0.08154, 0.19584, -0.06280, Temp-cm: inf Large VCM(group NA): 0.23298, 0.14145, 0.00921, Temp-cm: inf Large VCM(group NA): 0.22764, 0.09442, 0.07858, Temp-cm: inf Large VCM(group NA): 0.09441, 0.07206, 0.02138, Temp-cm: inf Large VCM(group NA): 0.00187, 0.04563, -0.03987, Temp-cm: inf Large VCM(group NA): 0.05896, 0.00550, 0.02418, Temp-cm: inf Large VCM(group NA): 0.2, 0.04126, 0.11459, Temp-cm: inf DD step 5199 vol min/aver 0.821 load imb.: force 1.3% How to Eliminate The Above error ? 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
[gmx-users] Aout Restraint on Water oxygen atoms
Dear Justin Thank you for your reply, I have set the Restraint Along the Z Axis . as follows #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] i funct fcx fcy fcz 1 1 0 0 100 #endif When i visualize The .gro file in VMD, Still The water Molecules Are Leaking in the Hydrophobic core . How to Avoid This? May I Decrease The fcz Value to 1000 ? -- 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] About Index Files
Dear Justin Thanks you for your Previous reply I am Following your Lipid Protein Tutorial When I try to create index File from .gro file obtained After genion EM (grompp) pro gramme Then I have got Repetition of Groups (from 1 to 11 11 to 21) in Command prompt 0 System : 15392 atoms 1 Protein : 714 atoms 2 Protein-H : 462 atoms 3 C-alpha : 42 atoms 4 Backbone : 126 atoms 5 MainChain : 168 atoms 6 MainChain+Cb : 210 atoms 7 MainChain+H : 210 atoms 8 SideChain : 504 atoms 9 SideChain-H : 294 atoms 10 Prot-Masses : 714 atoms 11 non-Protein : 14678 atoms 12 Protein : 714 atoms 13 Protein-H : 462 atoms 14 C-alpha : 42 atoms 15 Backbone : 126 atoms 16 MainChain : 168 atoms 17 MainChain+Cb : 210 atoms 18 MainChain+H : 210 atoms 19 SideChain : 504 atoms 20 SideChain-H : 294 atoms 21 Prot-Masses : 714 atoms 22 non-Protein : 14678 atoms 23 Other : 6250 atoms 24 DPPC : 6250 atoms 25 NA : 1 atoms 26 Water : 8427 atoms 27 SOL : 8427 atoms 28 non-Water : 6965 atoms 29 Ion : 1 atoms 30 DPPC : 6250 atoms 31 NA : 1 atoms 32 Water_and_ions : 8428 atoms I do not Know Why This Happens? Could You Please Suggest Any Solution? 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
[gmx-users] About Usage of Restraint
Dear Justin Thank you for your previous Mail Reply As you Instructed me in the Previous Mail to insert Vertical Restraint I Have increased Value of fcz to 10 While Should I make value of fcx and fcy to Zero ? otherwise may i Leave it as such #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcx fcy fcz 1 1 1000 1000 100 #endif I Have Followed the Following gromacs Hyper link to add vertical z axis Restraint http://www.gromacs.org/Documentation/How-tos/Position_Restraints Is My way is correct or Wrong? -- 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] About the Diffusion of Water Molecules
Dear Justin Thank you for your Previous reply, I am following your Protein -Lipid tutorial . I am doing simulation of Assembly of Cyclic Peptide ( Made up of Only Phenyl alanine Residue) in DPPC lipid . After I have Attained suitable APL (69 A^2) I solvated, neutralized (using genion) EMzed . Finally I Have Done NVT equilibration Using Restraint on all atoms of Lipid Molecules . At the End of My simulation I Have observed some of water molecules (60 water Molecules ) in Hydrophobic Part of Lipid Molecules (Amidst of Assembly of cyclic peptide) How to Avoid this ? Should Further Shrink APL using Perl And Then Proceeding NVT Equilibration ? -- 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] About Grid MAT
Dear Justin Thank you for your Previous Reply Mail I am using GridMAt MD Script When I run the APL Headgroup Calculation It runs well But I Have got Output With the Following Comment in My Command Prompt looking for offending protein atoms... There are 143 protein atoms within the headgroups of the top leaflet There are 65 protein atoms within the headgroups of the bottom leaflet To Avoid this Which Parameter Should I adjust Either precision Parameter or P_value Parameter 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
[gmx-users] About Lateral Diffusion of Lipids
Dear Justin Thank you for your Previous reply I am Following your Protein Lipid Tutorial When I do the msd analysis For protein in DPPC lipid-water Bilayer in lateral Z direction using P8 atoms as index Then I have Got the Following Output Is the Following My Out put is Reasonable or Not? Used 101 restart points spaced 10 ps over 1000 ps Fitting from 100 to 900 ps D[ P8] 0.0544 (+/- 0.0057) 1e-5 cm^2/s What Is Lateral Diffusion of Lipids ? Its Value for Membrane Protein (output ) indicates What ? Is there is Limiting (upper, Lower ) Value For Every System ? How could I come to a conclusion That My Value of My Diffusion Coefficient is Reasonable or Not 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
[gmx-users] About topology for cyclic petide
Dear justin Thank you for your Previous reply I Have Successfully constructed topology for cyclic peptide using spce bond and Other Appropriate Changes in the . top files Yet I Want to make CO Terminal But When I interactively Choose the Terminal By pdb2gmx It Shows Only 1)COO - 2)COOH 3)None I want to Make One more Choice Namely CO For C-Terminal Residue of (LAst Residue ) My Cyclic Peptide It Adds One Two oxygen atom on the Carbon Atom (O1 O2) . But I Need the Addition Of One Oxygen Atom How to Do It ? Which Database file Should I EDIT ? .C Terminal Data Base 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
[gmx-users] About construction of Cyclic peptide
Dear gromacs users I would Like to Construct a assembly of cyclic Peptide Is there is Any On line server or Tools Available ? Or any other Package Available It would be helpful if somebody Assists me Thanks In Advanve -- 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] About Packing of Lipids
Dear Justin , Thank you For your reply I am following your Protein lipids Tutorial . I have Reached APL 61.14 A^2 Then I did Em And NVT equilibration . As stated in your Tutorial . But After NVT Equilibration When I visualize My .gro File in VMD I have Observed approximately 20 water Molecules Nearer to Protein which is in the center of box I Think This is due to presence of some Hydrophilic Nature (Polar Nature) of Amino acids in my protein ? Is Such a diffusion of water from Hydrophilic Head Part towards polar residues of protein is Possible ? Otherwise this Behavior is odd ? May I continue NPT ? or Should I restrain the water in Z-Dimension During NVT? -- 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] About Diffusion of Water towards Protein in ceter of box
Dear Justin, Thank you for your Previous Reply To avoid the Diffusion of Water You Suggested me s follows The better approach would be a position restrain along the z-axis only, allowing the lipids to perhaps re-orient and pack a bit better, followed by NVT equilibration in the absence of any restraints on water. According to your Suggestion Should i Do the Two times Equilibration With restraint On water only in First NVT equilibration followed by another NVT equilibration without restraint on Water But Only With Lipids ? My Question is Can i simultaneously use Restraint for water and Lipids in Single NVT equilibration ? If i can My NVT equilibration is Successful (means No Diffusion of Water in the Tail Part.) But After That When I do NPT Equilibration There is Diffusion Of Some Water molecules Towards the protein in the center of box Not towards Tail of Lipids Is this Behavior is ODD or Normal ? If it is ODD May I again use the Restraint on Water During NPT Equilibration ? or May I continue the MD ? Thanks 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
[gmx-users] About Diffusion of water Towards Tail part of Lipids
Dear Justin, Than you for your Previous reply Regarding Diffusion Of Water From Head of Lipids to Tail Part During NVT Equilibration, You Suggested My one question as follows May I freeze these molecules During NVT Equilibration) ? The better approach would be a position restrain along the z-axis only, allowing the lipids to perhaps re-orient and pack a bit better, followed by NVT equilibration in the absence of any restraints on water. My Question is If Need to use Restraint on Water . Should I Generate Separate water_posre.itp using genrestr tool ? Otherwise May I Edit ( it means Applying restraint only in fcz column and Making Zero for fcx and fcy columns ) and use Default setting of restraint of water in .top files as follows #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcx fcy fcz 1 1 1000 1000 1000 #endif Also How to include this Restraint in .mdp just Like using -D Flag ? 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
[gmx-users] About Presence of Water in Hydrophobic core of lipids in NPT equlibration
Dear Justin, Thank you for your previous reply, I am doing Protein-Lipid simulation. After Em When I visualize the str in .vmd The water Molecules Present in Lipid (DPPC) Head groups .There is No Water Molecules Present in the Hydrophobic Part of Bilayer . While The Protein Is in the Center of box . Then I Have done NVT Equilibration When I visualize the .gro file in vmd Around 40 Water molecules (out of 2699 ) are present in Hydrophobic part of Lipid (that is Moving inside the box, Nearer to protein which is at the center) How to Avoid this ? May I simply delete these 40 water Molecules ? or May I freeze these molecules During NVT Equilibration) ? Can i Leave it as such and Then Proceed Further NPT? I Hope Your Valuable 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
[gmx-users] About Box VEctor
Dear Justin Thank you for your Previous Help Reply. I am Doing Protein Lipid Tutorial I Have Done Successive Shrinking (using inflate script) and EM until i reached APL (66.7 A^2) for DPPC in protein After Doing Sufficient Em and Shrinking steps I reaches box size of 6.81123 6.81123 5.0 At the End of Last EM May it Deviate from initial Box Size (5 5 5) ? 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
[gmx-users] About Box Vector
Dear Justin Thank you for your reply But For My system The Initial Value of Box Size is (5 5 5) Not equal to Final Box Value in both X and Y dimension 6.81123 6.81123 5.0 May Increase the Initial Box Size ? or otherwise May I Continue the Shrinking till t Have Reached The Initial Box Size if i Do this I Have Reached the APL Below 62A^2 Hoe to Solve this Problem? I hope on your Valuable Suggestion ? Further Information About My System Do u Need i Will tell? 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
[gmx-users] About Usage of maxwarn option in EM Afer first first Shrinking
Dear Justin Thank you For your Previous reply, For My system After First Shrinking Using Cut-off Value DPPC 18 perl inflategro.pl system.gro 4 DPPC 18 system_inflated.gro 5 area.dat Then I do the EM.During EM I need to use -maxwarn 1 option Otherwise I have got Error as follows in grompp If i use -maxwarn 1 then it runs Successfully May i use this -maxwan option in first Shrinking ? ./grompp_d -f emdppc.mdp -c system_inflated.gro -p 2KDQ.top -o 2KDQDPPCem.tpr Number of degrees of freedom in T-Coupling group rest is 19557.00 Largest charge group radii for Van der Waals: 1.201, 1.144 nm Largest charge group radii for Coulomb: 1.201, 1.144 nm WARNING 1 [file emdppc.mdp]: The sum of the two largest charge group radii (2.345197) is larger than rlist (1.20) Calculating fourier grid dimensions for X Y Z Using a fourier grid of 168x168x42, spacing 0.119 0.119 0.119 Estimate for the relative computational load of the PME mesh part: 0.92 NOTE 2 [file emdppc.mdp]: The optimal PME mesh load for parallel simulations is below 0.5 and for highly parallel simulations between 0.25 and 0.33, for higher performance, increase the cut-off and the PME grid spacing Fatal error: Too many warnings (1), ./grompp_d terminated. If you are sure all warnings are harmless, use the -maxwarn option. 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
[gmx-users] About The Diffusion of Water molecules in Protein Lipid Simulation
Dear Justin , Thank you for your Previous reply I am following your Protein Lipid Tutorial After Several Shrinking and several EM of my system i reached the APL for DPPC 64am^2 , I Have Added the ions to Neutralize the system . Then I have Done EM When I Visualize The system in VMD it was good As in the tutorial Web page Then I did NVT Equilibration , when i see the Resultant .gro file in VMD All the Lipid Molecules are just away from the protein ( which is Kept in center of Box) While some of the Water Molecules are nearer to Protein ( it means that during Equilibration water molecules are diffusing towards protein while Lipid Molecules are Diffusing Away from Protein Which is in the center) Is it correct or Wrong ? Where I have committed the Mistake ? Is my System Contains Voids ? Also Tail part of the Lipid molecules are protruding outside Box While Head part is in the Solvent Region (it means some Lipid Molecules Are flipped up) 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
[gmx-users] About The Diffusion of Water molecules in Protein Lipid Simulation
Dear Justin, With your Permission May I send the Equilibrated Structure to your Mail ID in Kindly Give ME Some Suggestion After Seeing my Structure? I am Eagerly Expecting your Positive Reply 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
[gmx-users] About APL And Shrunken System Size
I gave My cmd Prompt output for satisfactorily shrunken system as follows Reading. Scaling lipids There are 127 lipids... with 50 atoms per lipid.. Determining upper and lower leaflet... 64 lipids in the upper... 63 lipids in the lower leaflet Centering protein Writing scaled bilayer centered protein... Calculating Area per lipid... Protein X-min/max: 98 119 Protein Y-min/max: 99 117 X-range: 21 A Y-range: 18 A Building 21 X 18 2D grid on protein coordinates... Calculating area occupied by protein.. full TMD.. upper TMD lower TMD Area per protein: 3.75 nm^2 Area per lipid: 6.60886502362205 nm^2 Area per protein, upper half: 2.75 nm^2 Area per lipid, upper leaflet : 6.572858265625 nm^2 Area per protein, lower half: 3 nm^2 Area per lipid, lower leaflet : 6.67322109523809 nm^2 Writing Area per lipid... In the final Energy minimization (.gro file) of the satisfactorily shrunken system The Box vectors Has been Increased form 6 6 6 6 to 20.57700 20.57700 6.0 Then As you Told Me the There is Something wrong Because Such Large x-y Area is not Possible with Quoted APL ( 6.60886502362205 nm^2) May I Increase the Initial box size ? Why this Happens and Where I have Committed the Mistake ? My system is Cyclic Peptide I am grateful if you Give suggestion and Commments Thanks In Advance Done! -- 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] About BoxVector and APL
As uou Told me in the Previous Mail I have Given My sereis of Commands With Real file Names ./pdb2gmx_d -f 2KDQ.pdb -o 2KDQ.gro -ignh -ter -water spc ./editconf_d -f 2KDQ.gro -o 2KDQ_newbox.gro -box 6 6 6 -c ./editconf_d -f dppc128.pdb -o dppc128n.gro -center 3 3 3 -box 6 6 6 ./grompp_d -f emdppc.mdp -c dppc128n.gro -p topol_dppc.top -o emdppc.tpr -maxwarn 1 ./trjconv_d -s emdppc.tpr -f dppc128n.gro -o dppc128_whole.gro -pbc mol -ur compact ./editconf_d -f 2KDQ.gro -o 2KDQ_newbox.gro -box 6 6 6 -c cat 2KDQ_newbox.gro dppc128_whole.gro system.gro ./genrestr_d -f 2KDQ_newbox.gro -o strong_posre.itp -fc 10 10 10 perl inflategro.pl system.gro 4 DPPC 18 system_inflated.gro 5 area.dat ./grompp_d -f emdppc.mdp -c system_inflated.gro -p 2KDQ.top -o 2KDQDPPCem.tpr ./mdrun_d -v -deffnm 2KDQDPPCem perl inflategro.pl 2KDQDPPCem.gro 0.95 DPPC 0 system_inflated1.gro 5 area1.dat ./grompp_d -f emdppc.mdp -c system_inflated1.gro -p 2KDQ.top -o 2KDQDPPCem1.tpr ./mdrun_d -v -deffnm 2KDQDPPCem1 perl inflategro.pl 2KDQDPPCem1.gro 0.95 DPPC 0 system_inflated2.gro 5 area2.dat ./grompp_d -f emdppc.mdp -c system_inflated2.gro -p 2KDQ.top -o 2KDQDPPCem2.tpr ./mdrun_d -v -deffnm 2KDQDPPCem2 perl inflategro.pl 2KDQDPPCem2.gro 0.95 DPPC 0 system_inflated3.gro 5 area3.dat output for My satisfactorily shrunken system as follows Reading. Scaling lipids There are 127 lipids... with 50 atoms per lipid.. Determining upper and lower leaflet... 64 lipids in the upper... 63 lipids in the lower leaflet Centering protein Writing scaled bilayer centered protein... Calculating Area per lipid... Protein X-min/max: 98 119 Protein Y-min/max: 99 117 X-range: 21 A Y-range: 18 A Building 21 X 18 2D grid on protein coordinates... Calculating area occupied by protein.. full TMD.. upper TMD lower TMD Area per protein: 3.75 nm^2 Area per lipid: 6.60886502362205 nm^2 Area per protein, upper half: 2.75 nm^2 Area per lipid, upper leaflet : 6.572858265625 nm^2 Area per protein, lower half: 3 nm^2 Area per lipid, lower leaflet : 6.67322109523809 nm^2 Writing Area per lipid. ./grompp_d -f emdppc.mdp -c system_inflated3.gro -p 2KDQ.top -o 2KDQDPPCem3.tpr ./mdrun_d -v -deffnm 2KDQDPPCem3 In the final Energy minimization (2KDQDPPCem3.gro file) of the satisfactorily shrunken system The Box vectors Has been Increased form 6 6 6 6 to 20.57700 20.57700 6.0 As you're suspecting I may be confusing your files. In the beginning I am giving Series of Commands with Real files Name Could you Please Suggests Where i Have Confused in File Names ? Kindly Give me your Valuable 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
[gmx-users] About Doubt in Lipid protein Solvation
Dear Justin Thank you For your Previous Kind Reply I am following your Lipid-protein Tutorial for My system I Gave The Following Commands As Quoted in your Tutorial Also I Have Suitably Edited The Topology As in the Tutorial Now the Problem in My solvation . I Gave The Following Commands As Quoted in your Tutorial ./pdb2gmx_d -f 2KDQ.pdb -o 2KDQ.gro -ignh -ter -water spc ./editconf_d -f 2KDQ.gro -o 2KDQ_newbox.gro -box 6 6 6 -c ./editconf_d -f dppc128.pdb -o dppc128n.gro -center 3 3 3 -box 6 6 6 ./grompp_d -f emdppc.mdp -c dppc128n.gro -p topol_dppc.top -o emdppc.tpr -maxwarn 1 ./trjconv_d -s emdppc.tpr -f dppc128n.gro -o dppc128_whole.gro -pbc mol -ur compact ./editconf_d -f 2KDQ.gro -o 2KDQ_newbox.gro -box 6 6 6 -c cat 2KDQ_newbox.gro dppc128_whole.gro system.gro ./genrestr_d -f 2KDQ_newbox.gro -o strong_posre.itp -fc 10 10 10 perl inflategro.pl system.gro 4 DPPC 18 system_inflated.gro 5 area.dat ./grompp_d -f emdppc.mdp -c system_inflated.gro -p 2KDQ.top -o 2KDQDPPCem.tpr ./mdrun_d -v -deffnm 2KDQDPPCem perl inflategro.pl 2KDQDPPCem.gro 0.95 DPPC 0 system_inflated1.gro 5 area1.dat I Repeated the inflate and EM Until I have Attained APL 66 (Experimental value 62) At the End of EMinimised .gro file The Box vectors Has been Increased form 6 6 6 6 to 20.57700 20.57700 6.0 As result Box Size Also Increase When I solvate By mere Editing the Vanderwalls Radii to 0.470, then my system is is solvated By 64495 Water molecules How to Avoid this Problem ? This is too high Where I have Committed Mistakes I need your Valuable Ideas and Suggestions 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
[gmx-users] About Box vector and solvation
Dear Justin Thank you For you Previous reply. When I use inflate script There is Automatic Change in the box Vector At the End line of .gro file (output of inflate script) Then I have Done EM without Changing the Box Vector in the output of inflate script. in the screen i Have Observed the Following Discrepancy As follows . Step= 2, Dmax= 1.2e-02 nm, Epot= -7.91260e+04 Fmax= 2.30915e+03, atom= 6104 Step= 4, Dmax= 7.2e-03 nm, Epot= -7.93164e+04 Fmax= 7.83650e+03, atom= 85 Step= 7, Dmax= 1.2e-02 nm, Epot= -8.08972e+04 Fmax= 7.87323e+03, atom= 85 Step= 9, Dmax= 7.5e-03 nm, Epot= -8.11951e+04 Fmax= 3.15522e+03, atom= 85 It quits Step 3 ,4 and step 8 ( When i open em.log files Energy Corresponding to 3 and 4 As follows) Step Time Lambda Step Time Lambda Step Time Lambda 8 8.0 0.0 3 3.0 0.0 4 4.0 0.0 What it shows ? How to rectify this Problem ( I have used .mdp file in your Website) Can i change the box Vector in .gro file of EM output ( I cannot change Box vector in System_inflated .gro As you Told me) -- 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] About Keepbyz script for Deleting sol Molecules
Dear justin Thank you For your Previous reply, I am deleting The Water Molecules using keepbyz script as mailed me I want to keep waters around the head groups of my lipid, so How to Choose wisely upperz and lowerz values to my system ? 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
[gmx-users] About Removing excees Water molcules in Lipid Bilayer simulation
Dear justin, Thank you For your Previous reply I am doing Lipid -protein Bilayer simulation. As instructed in your tutorial i Have done Shrinking And EM .until i have Attained Area per Lipid 62.36A. Then I Have solvated as in the Tutorial ( using Vadradii 0.375) using Genbox tool As result My system has Solvated with 74496 Solvent Molecules . This is Too Higher for My system Is there is any Gromacs tools or other server or Package Available to delete Excess Water molecules . I wanted to Keep Water Molecules only on Either side of Bilayer While I need to Delete Water Molecules Nearer to Protein and deep inside the box ( box size 6 6 6) When i Try to solvate With Lower Number of Molecules ( 2000 Molcules) Which need to be Kept On either side of Bilayer , Then I need to Continue Shrinking process There by It is getting Over compressed ( Area Per Lipid Become Less than Experimental Value) Also When I solvate with Experimental APL 62A Then My system become over solvated ? How to rectify this Problem I Need to attain Both Correct APL and Solvated with Least Number of Molecules Only On either side of Lipid Bilayer 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
[gmx-users] About DPPC Cut-off
Dear justin Thank you for your previous reply, Finally I Have Found out problem When I Shrink My system Using Script The Size of the box at the end of System_inflated.gro file is not as i Have Assigned previously it has been Changed From Box size from 6 6 6 to 27 27 6.00 when I edit The end line of Output file Everything become Ok (when i Solvate it has been solvated with 1024 sol Molecules) Now Can i use different DPPC Cut-off Value (20 or 25 ) ? or Different Scaling Factors (instead 0.95) Because When i Use 14 for my System No Lipid Molecules has been Deleted Also There is sudden Shrink in APL When I go from first iteration and EM to Second Shrink ( from 93A to 4.7A) Why Such Drastic Fall of APL Occurs? How to Rectify this Problem? 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
[gmx-users] About Solvation of Lipid Protein
Dear Justin Thank you for your Previous reply I am following your Protein-lipid Tutorial ( KALP peptide in DPPC) In your tutorial How many Number of Water Molecules you needed to solvate Lipid -protein When I solvate The Number of Water Molecules are 57647 Is it Too high Or Ok 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
[gmx-users] About Diffusion of Solvent Molecules
Dear Justin, Thank you for your Previous reply. I am Extending your Protein Lipid tutorial To my System I am using DPPC128.pdb Which Surround the Cyclic Peptide. As You Quoted in tutorial I am Solvating My Lipid-protein Environment Using 148 Molecules (By genbox tools while I am using Vanderwalls Radii 0.92 for Carbon atom ) When I visualize .gro File in VMD Most of the water Molecules Are near the Face of My box ( Away from center) while Lipid molecules are concentrated Around Protein Which is at The center of box . After Second Phase Equilibration (After NPT ,Same Parameter ) When I see .gro file in VMD Most of Water Molecules moved inside the box ( Surround the Protein along with the Lipid molecules ) Is this Type of Diffusion of Solvent molecules is Usual or Not. What I mean Should it (Water Molcules) Be Nearer to face of the Box Throughout Entire MD . or Need not be like That? 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
[gmx-users] About EM for Lipid Protein Tutorila
Dear Justin Sorry for the inconvenience in the previous Mail . I am Much obliged for your Previous help Now I am following Your Lipid Protein Tutorial I am using DPPC128.pdb And I Have Downloaded the DPPC.itp and topol_DPPC.top When I run the energy Minimization (em.mdp Downloded form your website) for the this Lipid I have got Following error Warning: 1-4 interaction between 1256 and 1259 at distance 3.831 which is larger than the 1-4 table size 2.200 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file or with user tables increase the table size I am using Default .itp , .top (Down Loaded from website quoted by you) and Dppc.gro (created by Editconf tool) Why this error comes ? I Have not manually constructed .top for lipids May be there are several discussion about this error in Mailing Archive . Here You Have not mentioned this type of error in your website Where have i committed Mistake? 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
[gmx-users] About Em and Equlibration With Lincs Algorithim
Dear Justin Than you for your previous Reply I am doing EM for My cyclic peptide using following EM. MDP ; ions.mdp - used as input into grompp to generate ions.tpr ; Parameters describing what to do, when to stop and what to save integrator = steep ; Algorithm (steep = steepest descent minimization) emtol = 1000 ; Stop minimization when the maximum force 1000.0 kJ/mol/nm emstep = 0.01 ; Energy step size nsteps = 5 ; Maximum number of (minimization) steps to perform constraints = none ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist = 1 ; Frequency to update the neighbor list and long range forces ns_type = grid ; Method to determine neighbor list (simple, grid) rlist = 1.4 ; Cut-off for making neighbor list (short range forces) coulombtype = PME ; Treatment of long range electrostatic interactions rcoulomb = 1.4 ; Short-range electrostatic cut-off rvdw = 1.4 ; Short-range Van der Waals cut-off pbc = xyz ; Periodic Boundary Conditions Steepest Descents converged to machine precision in 2885 steps, but did not reach the requested Fmax 1000. Potential Energy = -2.88282144376129e+05 Maximum force = 1.2580887753e+03 on atom 107 Norm of force = 4.38175991068554e+01 i Have done Five time EM using emtol = 1000 Every Attempt became failed Then i planned to use emtol = 1500 In Previus Mail You Quoted the Possible emtol = 1000 For Most of Protein in Water But in My case it is not so Because the ring is so stained So I use emtol = 1500 it is converged Successfully as follows writing lowest energy coordinates. Steepest Descents converged to Fmax 1500 in 2868 steps Potential Energy = -2.88282144367798e+05 Maximum force = 1.31510551954873e+03 on atom 107 Norm of force = 4.39665399153860e+01 If I continue further NPT equlibration with Lincs Algorithim it shows Error aS follows Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 1167.301393, max 4514.205877 (between atoms 164 and 168) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 164 168 154.6 2.3463 690.8265 0.1530 164 168 154.6 2.3463 690.8265 0.1530 165 166 118.1 1.3451 224.6411 0.1530 165 166 118.1 1.3451 224.6411 0.1530 166 167 67.4 1.1731 86.2422 0.1530 166 167 67.4 1.1731 86.2422 0.1530 168 169 141.9 2.9836 281.9632 0.1230 168 169 141.9 2.9836 281.9632 0.1230 1 2 66.8 0.0735 2.3215 0.1000 1 168 59.8 2.7313 251.2519 0.1330 1 3 126.5 0.1241 2.3286 0.1470 156 157 96.0 0.1464 0.3827 0.1470 157 161 110.5 0.1604 0.4095 0.1530 157 158 95.9 0.1523 0.3563 0.1530 161 163 31.2 1.3955 148.8536 0.1330 161 162 81.6 0.1293 0.6410 0.1230 163 164 137.9 3.2852 517.7200 0.1470 163 164 137.9 3.2852 517.7200 0.1470 3 16 92.2 0.1534 2.8760 0.1530 3 4 93.9 0.1528 2.8694 0.1530 Back Off! I just backed up step0b_n1.pdb to ./#step0b_n1.pdb.1# Back Off! I just backed up step0c_n1.pdb to ./#step0c_n1.pdb.1# Wrote pdb files with previous and current coordinates starting mdrun 'L-22 CYCLIC PEPTIDE' 10 steps, 20.0 ps. Warning: 1-4 interaction between 166 and 168 at distance 2.841 which is larger than the 1-4 table size 2.400 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file or with user tables increase the table size step 0: Water molecule starting at atom 7007 can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. 124 125 111.2 0.1530 297.2103 0.1530 125 127 38.3 0.1530 0.1981 0.1530 121 123 98.7 0.1470 1978.8023 0.1470 119 121 139.2 0.1330 222.7882 0.1330 119 120 35.3 0.1230 0.1629 0.1230 106 119 33.3 0.1530 0.1945 0.1530 step 0: Water molecule starting at atom 6461 can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. Back Off! I just backed up step0b_n1.pdb to ./#step0b_n1.pdb.2# step 0: Water molecule starting at atom 2855 can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. Back Off! I just backed up step0c_n1.pdb to ./#step0c_n1.pdb.2# Wrote pdb files with previous and current coordinates Wrote pdb files with previous and current coordinates Wrote pdb files with previous and current coordinates How TO Rectify the above errror Even I I have Visualised the EM.gro file in VMD It seem to be good
[gmx-users] About Lincs Algorithim for Cyclic Peptide
Dear Justin Thank you For your Previous reply I have used the EM.gro file of Cyclic Peptide For NPT Equlibrartion Without using Lincs Algorithim it run Suceesfully But with Lincs Algorithm It shows Errror As follows Though I have reduce the time step relative constraint deviation after LINCS: rms 3069855679.355833, max 11186146428.941977 (between atoms 164 and 165) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 166 167 143.7 0.1935 179340257.0542 0.1530 166 167 143.7 0.1935 179340257.0542 0.1530 168 169 158.7 1.4560 636653487.7409 0.1230 168 169 158.7 1.4560 636653487.7409 0.1230 164 168 171.7 2.0007 1704071509.3304 0.1530 164 165 169.7 1.8838 1711480403.7811 0.1530 164 168 171.7 2.0007 1704071509.3304 0.1530 164 165 169.7 1.8838 1711480403.7811 0.1530 165 166 165.2 0.6922 762944969.2944 0.1530 165 166 165.2 0.6922 762944969.2944 0.1530 1 2 139.5 0.1011 1465776.5396 0.1000 1 168 169.4 1.1190 546331954.5273 0.1330 145 147 38.1 0.1330 0.1781 0.1330 step 0: Water molecule starting at atom 7265 can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. Back Off! I just backed up step0b_n1.pdb to ./#step0b_n1.pdb.2# Back Off! I just backed up step0c_n1.pdb to ./#step0c_n1.pdb.2# Wrote pdb files with previous and current coordinates Segmentation fault Normally The Gromacs Does Not Have terminal option for cyclic Peptide While constructing .top for Cyclic Peptide (By using pdb2gmx) As Advised By mark I Have Edited My initial pdb file final .top file compatible to cyclic Peptide (by Making Bond between first and Last residue And then Making proper angle,Dihedral and other factors) Now I am confident on that topology . Also Bond Between First and Last Residue Are Intact throughout Entire Dynamics ( Here I am Running Without Lincs Algorithm) My Question is Is it Reasonable and Meaningful To equilibrate And do Production MD Without Lincs otherwise Is My EM Not well Enough ? Because I am doing Three Cycles of EM Output is as follows Steepest Descents converged to Fmax 6800 in 2 steps Potential Energy = -2.08749539864389e+05 Maximum force = 6.52976950643761e+03 on atom 17042 Norm of force = 4.52145850945473e+02 But When I Equilibrate With Lincs still It Shows Bad contacts As Mentioned Above My NPT.mdp file are as follows title = NPT Equilibration define = -DPOSRES ; position restrain the protein ; Run parameters integrator = md ; leap-frog integrator nsteps = 10 ; 2 * 5 = 100 ps dt = 0.0002 ; 2 fs ; Output control nstxout = 1000 ; save coordinates every 2 ps nstvout = 1000 ; save velocities every 2 ps nstenergy = 1000 ; save energies every 2 ps nstlog = 1000 ; update log file every 2 ps ; Bond parameters continuation = no ; Initial simulation constraint_algorithm = lincs ; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained ;lincs_iter = 1 ; accuracy of LINCS ;lincs_order = 4 ; also related to accuracy ; Neighborsearching ns_type = grid ; search neighboring grid cels nstlist = 5 ; 10 fs rlist = 1.4 ; short-range neighborlist cutoff (in nm) rcoulomb = 1.4 ; short-range electrostatic cutoff (in nm) rvdw = 1.4 ; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling is on tcoupl = V-rescale ; Weak coupling for initial equilibration tc-grps = Protein Non-Protein ; two coupling groups - more accurate tau_t = 0.1 0.1 ; time constant, in ps ref_t = 310 310 ; reference temperature, one for each group, in K ; Pressure coupling is on pcoupl = Berendsen ; Pressure coupling on in NPT, also weak coupling pcoupltype = isotropic ; uniform scaling of x-y-z box vectors tau_p = 2.0 ; time constant, in ps ref_p = 1.0 ; reference pressure (in bar) compressibility = 4.5e-5 ; isothermal compressibility, bar^-1 ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr = EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = yes ; Velocity generation is on gen_temp = 310
[gmx-users] About Usage of Constraints
Dear justin Thank you for your previous reply I am running NPT Equlibration at 20 ps with dt 0.0002 in 10 steps Without usage of Lincs Algorithm and its related parameters it runs Successfully . But When I Increase dt from 0.0002 to 0.002 then I have got error as follows in grompp WARNING 1 [file 2KDQTR.top, line 71]: The bond in molecule-type Protein_chain_A between atoms 1 N and 2 H1 has an estimated oscillational period of 1.0e-02 ps, which is less than 5 times the time step of 2.0e-03 ps. Maybe you forgot to change the constraints mdp option. Then I have used the Lincs Algorithm and its related parameter Then I have got Error during Mdrun as follows I saw there Are Plenty Of discussion in Mailing list But I am Not Able to come to conclusion relative constraint deviation after LINCS: rms 0.015272, max 0.577865 (between atoms 120 and 122) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length Wrote pdb files with previous and current coordinates 129 131 39.1 0.1475 0.1664 0.1330 129 130 37.8 0.1191 0.1243 0.1230 125 126 38.5 0.1738 0.1508 0.1530 124 129 103.2 0.0962 0.9157 0.1530 124 125 124.3 0.1725 0.8648 0.1530 122 124 169.9 0.4717 2.5621 0.1470 122 123 168.0 0.2655 3.1890 0.1000 120 122 176.3 0.5957 7.3414 0.1330 120 121 172.8 0.5550 6.4843 0.1230 What does the Above Fact Indicates I mean the Problem is in Topology or in MD Parameter file ? With Regards S.Vidhyasankar -- 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] About Protein in Bilayer Simulation
Thank you Justin For Your Previous reply Finally Somehow I have Adjusted The Cut-Off and Grid Size and Inserted Protein in Lipid By Deleting some Lipid Molecules MY Question is 1) When I am Using inflategro Perl Script ,I need to Use Cut-off , Scaling Factor ,Grid size , Is there is Any Rule to Set up Suitable Factor (Aforesaid) For my System ? 2) I need to Use Only Protein Surrounded By Lipid Molecules . I Do not Want to use genion tool to insert water . Is it Possible ? and Is it Reasonable To do Direct Minimization, Equilibration, Production MD without Water ? Thanks In Advance S.Vidhya sankar With Regards S.Vidhya sankar -- 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] About pritein Lipid Bilayer Simulation
Dear Justin , Thank you for your Previous reply using Genbox I have Successfully Solvated Energy Minimized System_shrink.gro file It adds 84266 water molecules . Then Tutorial How to Check Existence of Water Molecules within HydroPhobic core of Bilayer it is Difficult to see and detect in VMD With Regards S.Vidhyasankar -- 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] About Lipid Protein simualtion
Dear Justin , Thank you for you Previous reply. I am doing Simulation of Cyclic Peptide in Lipids I am following your tutorial When I use inflategro script For my System I have got Output System_inflated.gro file with certain message in Command prompt as follows . The Below Message Shows That There is No Lipid Molecules Are Deleted Should I Change the Cut-off or scaling Factor to Delete the Lipid Molecules or is it enough , I Mean Must Some Lipid Molecules Need to be Deleted ? There are 128 lipids... with 50 atoms per lipid.. Determining upper and lower leaflet... 64 lipids in the upper... 64 lipids in the lower leaflet Centering protein Checking for overlap ...this might actually take a while 100 % done... There are 0 lipids within cut-off range... 0 will be removed from the upper leaflet... 0 will be removed from the lower leaflet... Writing scaled bilayer centered protein... Calculating Area per lipid... Protein X-min/max: 19 40 Protein Y-min/max: 21 39 X-range: 21 A Y-range: 18 A Building 21 X 18 2D grid on protein coordinates... Calculating area occupied by protein.. full TMD.. upper TMD lower TMD Area per protein: 4 nm^2 Area per lipid: 8.9375 nm^2 Area per protein, upper half: 3.5 nm^2 Area per lipid, upper leaflet : 8.9453125 nm^2 Area per protein, lower half: 3.5 nm^2 Area per lipid, lower leaflet : 8.9453125 nm^2 Writing Area per lipid... Done! 2) Also When I Run Grompp for EM Which Topology Should I use ? I have used my Multi chain protein.top When I Have used that I got Error AS follows Fatal error: [ file strong_porse.itp, line 8 ]: Atom index (4) in position_restraints out of bounds (1-3). This probably means that you have inserted topology section position_restraints in a part belonging to a different molecule than you intended to. In that case move the position_restraints section to the right molecule. For more information and tips for troubleshooting, please check the GROMACS How to Rectify the Problem? Thanks In Advance With High Regards S.Vidhyasankar -- 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] About Warning in grompp
Dear Gromacs users i am doing NPT Eqlibration for a cyclic peptide When I run grompp I have got Warning as follows WARNING 1 [file 2KDQ3.top, line 1137]: The bond in molecule-type Protein_chain_A between atoms 1 N and 2 H has an estimated oscillational period of 1.0e-02 ps, which is less than 5 times the time step of 2.0e-03 ps. Maybe you forgot to change the constraints mdp option. How to Rectify this Warning? If i Neglect using -maxwarn 1 option then have got Segmentation Fault during mdrun 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
[gmx-users] About Bond in Topology
Thank you Sir. For your repl I Would like to construct .top file for Cyclic Peptide . My N-terminal residue is ARG and C-Terminal is PRO . In pdb There is Bond between N atom of ARG (First residue) and C atom of PRO (Last Residue) When I Generated Topology using pdb2gmx . But there is No bond connectivity Between First and Last Atom .Then Manually I have Edited .top file and I have defined the bond Between First Atom (1) and Last atom (169) . Then I have done EM Successfully . My Question Is Will This Manual Editing of .top File create a bond or Not . With Regards S.Vidhyasankar -- 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] About Presence of Bond In Topology
Dear Justin Thank you for your Reply After pdb2gmx When i Visualize the resultant .gro file of my cyclic peptide in VMD I have Observed the Bond Between Nitrogen atom (N ) of First residue and Carbon atom (C) of Last residue I have not observed The same bond when I open and Visualize in Chimera . Then How Could i Confirm Whether the bond is present or Not? 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
[gmx-users] About Energy Minimisation
Dear Mark Thank you for your previous help With your Help I Have successfully Constructed .top and .gro for my cyclic peptide After That i Have solvated and added ions . . But when I do Energy Minimization My Molecule after Energy Minimization ( I have Visualized .gro file in VMD) The bond Between N atom of first Residue ( N-terminal) and C atom of last residue (C-terminal end) Has become Broken . How to Avoid this ? 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
[gmx-users] About topology construction for yclic pepetide
Dear Mark , Again Thanks for you reply After Editing my pdb file from intial FL to FLF format Then i Run pdb2gmx for my linaer pdb file , i have selected none for both termini ( with -ter option) as you mailed me in the previous mail I have got error as follows Fatal error: There is a dangling bond at at least one of the terminal ends. Select a proper terminal entry. How to Rectify this error For your Remembrance i pasted your previous Discussion 1) Take your initial coordinate file, make a copy and in it make a copy of the first residue and place it after the last residue, taking care to obey the format of the file you're using, and update things like atom counts and atom and residue indices. The coordinates of the copied atoms don't matter. Now you have a coordinate file for FLF. 2) Process that with pdb2gmx using -ter and choosing none. This has built a linear topology for FLF, with a correct L-to-F link for you to use as a template for making a cyclic FL. 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
[gmx-users] About topology construction for Cyclic peptide
Dear Mark, Thank you for your reply I have used the peptide FLF For that pdb2gmx construct topology successfully with -ter choosing any thing for both terminal. But When i Choose none with -ter for both terminal It again shows error as follows Fatal error: There is a dangling bond at at least one of the terminal ends. Select a proper terminal entry. For your Convenience i have pasted the previous discussion That suggests you have a problem with your coordinate file that is independent of your attempt to cyclize. Can you generate a topology for FL with a) -ter choosing none, b) -ter choosing anything else? With Regards S.vidhyasankar -- 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] About EM for Cyclic Peptide
Dear Mark Thank your excellent and patience Reply. it is very useful I Did as you Instruct in Gromacs Mailing List But when I DO Energy Minimization I have got following error Steepest Descents converged to machine precision in 31 steps, but did not reach the requested Fmax 1000. Potential Energy = -nan Maximum force = 1.36683186708214e+07 on atom 26 Norm of force = -nan Even I have Adjusted the Various Parameters Namely emtol and emstep still the same thing is repeated -- 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] Pdb2gmx for cyclic Peptide
Dear Justin Thanks Again for your reply When I run Pdb2gmx using -ter option for my Cyclic peptide and i have selected None for both termini as you instruct in the previous mail i have got error as follows Fatal error: There is a dangling bond at at least one of the terminal ends. Select a proper terminal entry. How to resolve these error For you remembrance i have pasted the previous mail Discussion I am doing MD Cyclic Peptide When I run pdb2gmx , The Conect Infromation in pdb file are ignored . so that it is not able to connect the first and last residue in cycle . But it construct and .top and.gro files successfully while in .gro file the end residues are closed as NH3+ and COO-(charge) (it means there is Bond between Nitrogen and carbon atom) It consider the N atom of first residue as NH3+ and C atom as COO-(charge) but I need to take N as peptide Nitrogen and C as Peptide carbon What Should i do to invoke conect information when i run pdb2gmx tool Use the -ter option and choose None for both termini.( Your Ansewr) Also Can i Directly Edit (it means removing excess hydrogen and oxygen atom by ; symbol) .top an .gro files and can i use to proceed further ? No. This will cause errors in the [moleculetype] numbering and all successive (Your Answer) directives. Re-run pdb2gmx instead. Thanks in Advance With Regards S.vidhyasankar -- 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] About pdb2gmx for cyclic pepetide
Dear Justin and other Gromacs users , Thank you for your previous reply Again i Have tried the option -missing when i use pdb2gmx tool i have got errror as follows My command is ./pdb2gmx_d -f 2KDQ.pdb -o 2KDQ.gro -p 2KDQ.top -missing -ignh -ter There is a dangling bond at at least one of the terminal ends. Select a proper terminal entry. I went through a Mailing Archive Yet no body explain the proper Topology construction for cyclic peptide It Discussed about Manual editing of topology But in my case it is headache Because my cyclic peptide contains large number of atom How to solve this problem without manual editing With Regards S.vidhyasankar -- 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] Reg pdb2gmx for Cyclic peptide
Dear Justin Thank you for your Previous reply, sorry for the inconvenience to you personal Mail. I am doing MD Cyclic Peptide When I run pdb2gmx , The Conect Infromation in pdb file are ignored . so that it is not able to connect the first and last residue in cycle . But it construct and .top and.gro files successfully while in .gro file the end residues are closed as NH3+ and COO-(charge) (it means there is Bond between Nitrogen and carbon atom) It consider the N atom of first residue as NH3+ and C atom as COO-(charge) but I need to take N as peptide Nitrogen and C as Peptide carbon What Should i do to invoke conect information when i run pdb2gmx tool Also Can i Directly Edit (it means removing excess hydrogen and oxygen atom by ; symbol) .top an .gro files and can i use to proceed further ? 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
[gmx-users] About Bond breaking and usage of constraints
Dear justin , Thank you fro your Reply I am doing MD for Cyclic poly Peptide With ARG as N-termina and PRO as C-terminal . I have run pdb2gmx it is oak. . I have solvated and added ions successfully But when i Run the Energy Minimization The Bond between N atom of ARG and C atom of PRO is broken . What Should i Do To keep this Bond Through entire EM and MD ? Can i Use Constraints option in topology file if i need to use Constraints option What is the Syntax ? Also The Bond is not constructed between N atom and C atom of terminal ARG and PRO residues in Topology -- 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] About Number of Components of eigen Vector
Dear justin Thank you for your gem of Reply I am doing ED. With respect to my all 900 C-alpha atoms So I have used the output of g_covar namely eigvec.trr as input to g_anaeig_d as follows g_anaeig_d -v eigenvec.trr -comp eig1.xvg -first 1 -last 3 -xvg none I have obtained eig1.xvg i am using First three eigen Vector My Doubt is Are these three Eigen vector is divided in to three Components or Four components because My eig.xvg contains four segment for Each vector , Each segment ending with symbol follows @ xaxis ticklabel start type spec @ xaxis ticklabel start -0 @ yaxis tick major 0.1 @ yaxis tick minor 0.05 @ yaxis ticklabel start type spec @ yaxis ticklabel start -0.1 @ zeroxaxis bar on @ zeroxaxis bar linestyle 3 1. 0.03973 2. 0.03619 . . 1. -0.03491 2. -0.03068 . . . 1. -0.01246 . . 1. -0.01428 . . Thanks In Advance -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] About Shake and Lincs Algorithm
Dear Justin , Thank you for your Previous useful reply I Have used the Lincs Alogrithim for NPT Equlibration MD. But For Main MD I would like to use Shake Algorithim With Shake _tol = 0.1 with continuation = yes Is it Correct to use two algorithm for simulation of same system (NPT, longMD) To which extent Will it Affect the result (Free energy)? Because I am doing Free energy calculation Based on Essential Dynamics ? Is it possible Thanks In advance With Regards S.Vidhyasankar -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] (no subject)
Dear Gromacs user , I Write Some linux .sh programming to automate grompp and mdrun process in Clustering which is as Follows Could Any one of you point out the error in following script files ? is it correct or not. #!/bin/bash #! -l nodes=1:ppn=4 # load the modules # preproc source=/usr/local/plumedmpigromacs/bin GROMPP=/usr/local/plumedmpigromacs/bin/grompp_mpi_d MDRUN=/usr/local/plumedmpigromacs/bin/mdrun_mpi_d $GROMPP -f npt_umbrella.mdp -c conf0.gro -p topol.top -n index0.ndx -o 232npt0.tpr -maxwarn 1 -po mdout0.mdp /dev/null mpirun -np 4 $MDRUN -deffnm 232npt0 -cpi 232npt0_prev.cpt /dev/null #exit # preproc source=/usr/local/plumedmpigromacs/bin GROMPP=/usr/local/plumedmpigromacs/bin/grompp_mpi_d MDRUN=/usr/local/plumedmpigromacs/bin/mdrun_mpi_d $GROMPP -f npt_umbrella.mdp -c conf153.gro -p topol.top -n index153.ndx -o 232npt153.tpr -maxwarn 1 -po mdout153.mdp /dev/null mpirun -np 4 $MDRUN -deffnm 232npt153 /dev/null #exit Thanks in Advance With Regards S. Vidhya sankar -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] About EM Error (simulation exploding)
Dear Justin, Thank you for your Previous Reply. I have got the following Error in EM using steepest Descent method in gromacs Warning: 1-4 interaction between 4728 and 4733 at distance 3.030 which is larger than the 1-4 table size 3.000 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file or with user tables increase the table size I know That my System is exploding .I have checked that my ouput .gro file in VMD there is No error . in my system. Then What KInd of Physical Parameter lead to error My box size is ./editconf_d -f 1OG2O.gro -o 1OG2Onewbox1.gro -center 7.0 8.0 7.0 -box 14.0 16.0 14.0 my Em.mdp file as follows integrator = steep emtol = 1000 emstep = 0.01 constraints = none nsteps = 5 nstlist = 1 ns_type = grid rlist = 2.0 coulombtype = PME rcoulomb = 2.0 rvdw = 2.0 pbc = xyz Is there is any contradiction. between box Size and .mdp parameters I am sure There is No error in .top and .gro file Then what could be the Source of error Thanks in Advance With Regards S.Vidhyasankar -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] About EM
Dear gromacs user, Thank you for your previous reply. i am doing Energy minimization using Steepest Descent method . When i do that i got the following error r Steepest Descents converged to machine precision in 35 steps, but did not reach the requested Fmax 40. Potential Energy = -nan Maximum force = 2.23324790984423e+09 on atom 9566 Norm of force = -nan How to rectify the above error? With Regards S.Vidhya sankar -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] About pdb2gmx
Dear Justin Thank you for your previous reply When i run the .pdb2gmx_d -f 1OG2O.pdb -o 1OG2O.gro -p 1OG2O.top -renum It runs successfully. But i have on issue. My PDB contains HIS residues in both chain A and B I have selected GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656) The .rtp file of this force field does not contain any [ HIS ] residue so it takes HIS as HISE as shown in the cmd prompt will ti leads to any poor construction of topology and .gro files ? . How to solve this error? Analysing hydrogen-bonding network for automated assigment of histidine protonation. 682 donors and 670 acceptors were found. There are 849 hydrogen bonds Will use HISE for residue 78 Will use HISE for residue 184 Will use HISE for residue 230 Will use HISE for residue 251 Will use HISE for residue 276 Will use HISE for residue 316 Will use HISE for residue 344 Will use HISE for residue 353 Will use HISD for residue 368 Will use HISE for residue 396 Will use HISE for residue 410 Will use HISE for residue 411 Will use HISE for residue 411 Identified residue PRO30 as a starting terminus. Identified residue HIS411 as a ending terminus. 8 out of 8 lines of specbond.dat converted successfully Processing chain 2 'B' (3702 atoms, 462 residues) Analysing hydrogen-bonding network for automated assigment of histidine protonation. 682 donors and 670 acceptors were found. There are 830 hydrogen bonds Will use HISE for residue 78 Will use HISE for residue 184 Will use HISE for residue 230 Will use HISE for residue 251 Will use HISE for residue 276 Will use HISE for residue 316 Will use HISE for residue 344 Will use HISE for residue 353 Will use HISD for residue 368 Will use HISE for residue 396 Will use HISE for residue 410 Will use HISE for residue 411 Will use HISE for residue 411 Identified residue PRO30 as a starting terminus. Identified residue HIS411 as a ending terminus. 8 out of 8 lines of specbond.dat converted successfully Thanks in Advance With Regards S.Vidhyasankar -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] Mopac gomacs installation
Dear Gromacs user I am trying to install Mopac gromacs . i have folloed the instruction as in the web page I used the following command LIBS=-lmopac LDFLAGS=-L/usr/local/lib ./configure --with-qmmm-mopac --enable-double --program-suffix=_d It configured successfully But when i compile using make command i Got the follwing error /root/gromacs-4.5.51/src/mdlib/.libs/libmd.so: undefined reference to `domldt_' /root/gromacs-4.5.51/src/mdlib/.libs/libmd.so: undefined reference to `domop_' collect2: ld returned 1 exit status make[3]: *** [grompp] Error 1 make[3]: Leaving directory `/root/gromacs-4.5.51/src/kernel' make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory `/root/gromacs-4.5.51/src' make[1]: *** [all] Error 2 make[1]: Leaving directory `/root/gromacs-4.5.51/src' I have kept in libmolac.a files (pre compiled library files) in usr/local/lib even i used the CPPFLAGS Does anybody give suggestion about the wrong things that i have done ? Thanks In advance -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] jalem...@vt.edu
Dear Justin Thank you for your previous reply How to solve error obtained when i invoke command as follows ./setupUmbrella.py summary_distances.dat 0.2 run-umbrella.sh caught-output.txt I got error as follows in Caught_output .txt File ./setupUmbrella.py, line 182, in module out = main() File ./setupUmbrella.py, line 150, in main distance_table = readDistanceFile(distance_file) File ./setupUmbrella.py, line 49, in readDistanceFile value = float(columns[1]) IndexError: list index out of range As you mailed me in previous mail i showed the dist.xvg file also i have obtained this .xvg file through your Distance.pl script It contains as follows This file was created Sun Jun 17 19:23:40 2012 # by the following command: # g_dist_d -s 0.154protopull.tpr -f conf143.gro -n index3.ndx -o dist143.xvg # # g_dist_d is part of G R O M A C S: # # Great Red Owns Many ACres of Sand # @ title Distance @ xaxis label Time (ps) @ yaxis label Distance (nm) @TYPE xy @ view 0.15, 0.15, 0.75, 0.85 @ legend on @ legend box on @ legend loctype view @ legend 0.78, 0.8 @ legend length 2 @ s0 legend |d| @ s1 legend d\sx\N @ s2 legend d\sy\N @ s3 legend d\sz\N 143.000 0.5957624 0.0363277 -0.0382985 0.5934192 Like above several dist file i have obtained as dist25.xvg, dist130.xvg, dist158.xvg Also i have one doubt What is the difference between .xvg file obtained by both distance.pl script and g_dist tool Can i use the .xvg file obtained through g_dist command as summary_distance.dat by mere renaming .xvg file 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
[gmx-users] About Mike Harms python script
Dear justin Thank you for your previous reply I am doing Umbrella sampling in gromacs I have 30 set of initial configuration in .gro file format .Now i would like to do NPT equilibration and umbrella sampling for all these configuration (for these i have to carry out 30 times equilibration and 30 times umbrella sampling) to Automate these process i used the python script provided by Mike Harms. but when invoke the command as follows ./setupUmbrella.py summary_distances.dat 0.2 run-umbrella.sh caught-output.txt I got error as follows in Caught_output .txt Traceback (most recent call last): File ./setupUmbrella.py, line 182, in module out = main() File ./setupUmbrella.py, line 150, in main distance_table = readDistanceFile(distance_file) File ./setupUmbrella.py, line 49, in readDistanceFile value = float(columns[1]) IndexError: list index out of range I have all the required files ( index.ndx files , dist.xvg files, , .gro files and .mdp files) in the running directory How to solve these error 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
[gmx-users] About Umbrella sampling
Dear justin Thank you for your previous Valuable reply. To do umbrella sampling should i run more number of steps than i run in Umbrella pulling ? otherwise if i use lesser number of steps in Umbrella sampling than pulling will it affect result Is there is any rule between number of steps and dt in umbrella pulling and umbrella sampling? 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
[gmx-users] About gomacs MPI installation
Dear justin Thank you for your previous reply Now i am trying to run the parallel gromacs simulation (gromacs 4.5.5) first of all i have successfully installed debain package of gromacs-openmpi for that i have configured and compiled using the following command ./configure --enable-mpi --enable-double --prefix=/usr/local/mpigromacs --program-suffix=_mpi_d then I issued the make make mdrun make install make install-mdrun It compiles nicely and successfully I have few doubt 1) should i need to install both rpm of openmpi (coresponding to my OS) and Debain of gromacs-openmpi ? (compatible to my Linux OS) Now i have both Otherwise is it enough to install only Debain gromacs-openmpi to install gromacs in paralleel 2) how to check Wheather Parallel installation of gromacs ? wheater is installed parallely or not? I have installed on single Hyper threading supported intel pentium i5 (dual core processor,four thread) it means i amusing thread based parallelism not mpi based parallelism (i know the performance may be poor, though later i will extend this to clustering) please tell me The Above my understandings is correct or not if ther are any wrong things in the compilation procedure Please give me some tips to rectify error? I am very grateful to your valuable reply Also if the above procedure is correct Can i run the gromacs parallel simulation using the following command mdrun_mpi_d -nt 8 -s topol.tpr Don't i Need mpirun command ? Thanks in Advance With regards S.vidhyasankar-- 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] About usage of node in mpi calculation
Dear justin , Very very thanks for your previous patience reply When i run the mpi calculation using more than one node (each node have 16 processor) which option do i need to use in the following command may i use -npme option? mpirun -np 19 mdrun_mpi_d -s toplo.tpr Thanks in Advance S.Vidhyasankar -- 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] About Umbrella spacing
Dear justin thank you for your reply. i Have got Summary_distance.dat file as output I need 0.02 nm Spacing For that I Inspect Output .Dat file For some Distance i Have not obtained corresponding Coordinate files Example as follows After 148th frame I have not received a Coordinate file corresponding to 0.623145, i am getting only 0.6353225 which corresponds to 150th frame It means spacing is not uniform Now what to do to get coordinate files corresponding to equal spacing frame Coordinates 139 0.5839833 148 0.6008763 150 0.6353225 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
[gmx-users] About Distance.pl script
Dear justin , Thank you for your previous reply When i Download and run Distance.pl script In your website I got the following error readline() on closed filehandle IN at ./Distance.pl line 16. Use of uninitialized value $distance in concatenation (.) or string at ./Distance.pl line 30. How to rectify this error ? Thanks in Advance With regards S.Vidhyasankar-- 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] About desired Spacing in Distance.pl script
Dear justin Thank you for your at once reply I have successfully use the Distance.pl I got output. .But in Distance.pl script i have not represented the Any Desired spacing (0.3nm) . Should i Represent? . If i need to represent Where Should i represent in Distance .pl script file?-- 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] Abot genbox and editcon
Dear justin Thank you for your previous reply I have solvated my protein molecule with specific number of water molecules By keeping the protein (solute) at center of box (option available in editconf) but when i visualize the resultant .gro file in VMD the solute molecule are not closely surrounded by water moleculesi need Solute molecules to be closely surrounded by solvent molecules without changing the dimension of box i am using Cubic box is there is any option in available in gromacs With Cheers S.vidhyasankar 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
[gmx-users] genbox
Hello Justin, Thanks for your patient reply I would like to solvate my molecules with specific number of water molecules what option is a suitable to do that ? in editconf with regards S.Vidhya sankar -- 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] About solvation
Dear Mark Thank you for your reply. I did As u said But when I visualize the resulting .gro files in VMD .The solute molecules are centered (i used the center option in editconf) But solvent molecules are are away . but within the box i need Solute molecules to be closely surrounded by solvent molecules . Is there is Any way to do this ? 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
[gmx-users] About spacing in umbrella sampling
Dear justin, Thanks for your previous reply which one is reliable to get desired spacing in umbrella sampling either from output of g_dist or from pullx.xvg? If i choose spacing from pullx.xvg will it affect the result ? (poor sampling and poor free energy calculation). 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
[gmx-users] About restraints
Dear Plumed gromacs user Does any body know How to set restraint suitably in umbrella sampling using plumed -gromacs ? i am using plumed for umbrella sampling 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
[gmx-users] about umbrella sampling
Dear Justin, Thank you for your immediate reply amidst of your busy schedule I am trying to pull one of chain of my protein using umbrella option of gromacs (As did in your website tutorial) After umbrella pulling i have extracted all frame of .gro from .trr files . i am getting various .gro files.As stated in tutorial i am using g_dist command it shows progression of COM between Chain A(Mobile group) and Chain_B ( Reference group). i have not used the Perl script using Distance.xvg files (Obtained as output of g_dist) Can i select spacing for sampling.? The above My Assumption is wright or wrong.?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
[gmx-users] About Choice PDB
Dear justin,, Thank you for your immediate reply. Which PDB is suitable Either X-ray PDB (brookavean protein data bank) or NMR PDB to study the effect of ionic strength on protein. If i use x-ray PDB will it affect the result though i solvate and neutralise the PDB before energy minimization, Equilibration and MD ? 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
