[gmx-users] gangle command
Dear Gromacs users I want to calculate the angle between P-N vector in the head group of DPPC molecules with the z-axis (bilayer normal) using gangle command.I know that for the z axis I should use (-g2 z) but do not know how to define a vector for P-N. Your help would be greatly appreciated. Regards Delara -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] How to define a vector for gangle command
Dear Justin Many thanks for your reply. My problem is not with the z axis. I use -g2 z for that as you mentioned. I do not know how to define a vector for P-N vector. Help me on this please. Thanks in advance Sincerely Delara On Wednesday, 30 May 2018, 16:19:18 GMT+4:30, Justin Lemkul wrote: On 5/30/18 4:06 AM, delara aghaie wrote: > Dear Gromacs users > My simulation box contains dppc lipid bilayer containing a membrane protein. > I want to calculate the angle between P-N in dppc head group and the bilayer > normal (z-axis). > We want to use the gromacs gangle command for this purpose. > > The command asks us to define a vector for P-N, while for the axis z it does > not require vector definition. > I can make an index group containing all the P and N atoms of the dppc > headgroup, but I do not know how to make a vector from these two endpoints to > give it to the gangle command for angle calculation. Use gmx gangle -g2 z -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] How to define a vector for gangle command
On Wed, 30/5/18, Justin Lemkul wrote: Subject: Re: [gmx-users] How to define a vector for gangle command To: gmx-us...@gromacs.org Date: Wednesday, 30 May, 2018, 11:48 Dear Justin Many thanks for your reply. My problem is not with the z axis. I use -g2 z for that as you mentioned. I do not know how to define a vector for P-N vector. Help me on this please. Thanks in advance Sincerely Delara On 5/30/18 4:06 AM, delara aghaie wrote: > Dear Gromacs users > My simulation box contains dppc lipid bilayer containing a membrane protein. > I want to calculate the angle between P-N in dppc head group and the bilayer normal (z-axis). > We want to use the gromacs gangle command for this purpose. > > The command asks us to define a vector for P-N, while for the axis z it does not require vector definition. > I can make an index group containing all the P and N atoms of the dppc headgroup, but I do not know how to make a vector from these two endpoints to give it to the gangle command for angle calculation. Use gmx gangle -g2 z -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] How to define a vector for gangle command
Dear Gromacs users My simulation box contains dppc lipid bilayer containing a membrane protein. I want to calculate the angle between P-N in dppc head group and the bilayer normal (z-axis). We want to use the gromacs gangle command for this purpose. The command asks us to define a vector for P-N, while for the axis z it does not require vector definition. I can make an index group containing all the P and N atoms of the dppc headgroup, but I do not know how to make a vector from these two endpoints to give it to the gangle command for angle calculation. Your help would be greatly appreciated. Best regards Delara -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] problem in simulation mutant p53 protein both in swiss pdb viewer and energy minimization with gromacs
Dear Gromacs Users I want to simulate human p53 protein and two of its mutants to see how mutation affect its structural properties. I obtained the nature and mutant pdb files form protein data bank. when I submitted the mutant files to pdb2gmx command it gave error on misiing atoms. I fixed the pdb files using swiss pdb viewer. There is an optin in this program which minimizes the energy of pdb file, but when I wanted to minimize the energy of mutant pdb file, I got error. You can see the error in attached files. (I hhave attached the image of error page) After seeing this error, I decided to ignore this stage and submit the mutant pdb file, taken from swiss pdb viewer to pdb2gmx command. When I did that, I did not get error and decided to acceot the energy minimization using gromacs instead of the swiss pdb viewer. Now the questions: 1) how can I fix the error by swiss pdb viewer? 2) Is it right to take pdb file with out energy minimizing from swiss pdb viewer and submit it for simulation to gromacs? - The nest problem is that when I submitted the mutant pdb file taken from swiss pdb to pdb2gmx and it worked successfully, then I made the simulation box and added the required ions according to hustin lyzozyme tutorial. When I did energy minimization I got strange output files besides the regular ones: the name of those files are: step14b_n0.pdb step14c_n0.pdb step15b_n4.pdb step15c_n4.pdb It would be greatly appreciated if you let me know what are these files and what I should do about them? can I continue the simulation by just ignoring them? Thanks in advance Best regards D.M -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] please guide me through the confusing gromacs results!!!
Dear Gromacs users, we want to simulateHSA protein using8 processors. Usually with our available system 10ns simulation on 8 processors lasts 2-3 days. This time we submitted 10 ns simulation, after almost 6 days it has finished but when we look at md.log file, only 179411 steps has been completed and all the averages are over this time, although we have submitted the run 500 steps=10ns 1) First I want to know how the log file shows the end of simulation, although only 0.35 ns of simulation is done and if we draw RDF the time again shows completing of 0.35 ns. you can see the ending part of log file below: 2) the second point is that the average load imbalance is shown as 110.3% while for previous runs we had this as 3-4 %. what can be the reason for this high load imbalance? and is this responsible for the lower simulation efficiency and higher time? and the most important that why the log file is written in the way that the simulation has been completed while only 0.3 ns has passes? Thanks for your time ** D O M A I N D E C O M P O S I T I O N S T A T I S T I C S av. #atoms communicated per step for force: 2 x 97992.1 av. #atoms communicated per step for LINCS: 2 x 2373.8 Average load imbalance: 110.3 % Part of the total run time spent waiting due to load imbalance: 1.4 % R E A L C Y C L E A N D T I M E A C C O U N T I N G Computing: Nodes Number G-Cycles Seconds % --- Domain decomp. 8 35882 556174.638 209101.4 5.1 DD comm. load 8 359 235.791 88.6 0.0 Comm. coord. 8 179411 407595.614 153241.1 3.7 Neighbor search 8 35883 39333.698 14788.0 0.4 Force 8 179411 205203.393 77149.0 1.9 Wait + Comm. F 8 179411 471040.171 177093.9 4.3 PME mesh 8 179411 8699277.459 3270611.0 79.1 Write traj. 8 752 15563.463 5851.3 0.1 Update 8 179411 12991.140 4884.2 0.1 Constraints 8 179411 438837.169 164986.8 4.0 Comm. energies 8 35884 149298.111 56130.6 1.4 Rest 8 6090.776 2289.9 0.1 --- Total 8 11001641.424 4136215.9 100.0 --- --- PME redist. X/F 8 358822 1446552.180 543850.9 13.1 PME spread/gather 8 358822 820940.059 308643.5 7.5 PME 3D-FFT 8 358822 6426689.995 2416201.0 58.4 PME solve 8 179411 5033.523 1892.4 0.0 --- Parallel run - timing based on wallclock. NODE (s) Real (s) (%) Time: 517026.991 517026.991 100.0 5d23h37:06 (Mnbf/s) (MFlops) (ns/day) (hour/ns) Performance: 9.634 506.361 0.060 400.250 Finished mdrun on node 0 Tue Feb 25 13:34:48 2014 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] error on running job in parallel
Dear gromacs users, Hello, here in our university the gromacs is installed parallel and now we are going to submit our simulation projects. To do a protein simulation, we are in the step to submit nvt and npt runs. this is the job,sh file which we use to submit our jobs: below you can see the explanation sent by the instructor: ++ Right now you can submit a job to chemistry queue, please make a job journal file( for example job.sh). Here is the sample required scripts: #!/bin/sh #$ -cwd #$ -j y #$ -S /bin/sh #$ -pe orte 8 cd $HOME mpirun -v mdrun -s topol.tpr -pe orte 8 specifies the number of core assigned to your job. (in this case 8 cores) After that submit your job to chemistry queue by this command: qsub -q chemistry.q job.sh + I have made the job.sh file and submitted the job using the above qsub command, but I get this error: Unable to read script file because of the error: ERROR! invalid option argument "-s" what should I do about this error??? Thanks in advance Regards D.M -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] missing residues in pdb file
Dear Gromacs users, I am going to simulate human serum albumin( HSA) .. The pdb file contains warfarin as well. Now I have two questions: 1) to delete warfarin which lines should be removed? only those starting with HETATM or more??? 2) in the pdb file I see this pART : EMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 ASP A 1 REMARK 465 ALA A 2 REMARK 465 HIS A 3 REMARK 465 LYS A 4 REMARK 465 LEU A 583 REMARK 465 GLY A 584 --- I want to know if I should add the missing residues before submitting the file to pdb2gmx command? The other thing is that when I run pdb2gmx, only I get this error: ( does the error says that there is something wrong with line 491? if so then what about that missing residues which I have not done anything about them???/ -- Program pdb2gmx_d, VERSION 4.5.5 Source code file: futil.c, line: 491 File input/output error: 2BXD.pdb For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors - -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
