[gmx-users] parallel simulation
I would like to run one simulation in parallel so that it utilises all the available nodes and cores. For that, I have compiled gromacs with mpi enabled and also installed openmpi on my machine. I am using the following command: mpirun -np 4 mdrun_mpi -v -s *.tpr When i use top command, I get: PID USER PR NI VIRT RES SHR S %CPU %MEMTIME+ COMMAND 22449 root 20 0 107m 59m 3152 R25 2.9 0:05.42 mdrun_mpi 22450 root 20 0 107m 59m 3152 R25 2.9 0:05.41 mdrun_mpi 22451 root 20 0 107m 59m 3152 R25 2.9 0:05.41 mdrun_mpi 22452 root 20 0 107m 59m 3152 R25 2.9 0:05.40 mdrun_mpi Similarly when i use mpirun -np 2 mdrun_mpi -v -s *.tpr, I get PID USER PR NI VIRT RES SHR S %CPU %MEMTIME+ COMMAND 22461 root 20 0 108m 59m 3248 R 50 3.0 5:58.64 mdrun_mpi 22462 root 20 0 108m 59m 3248 R 50 3.0 5:58.56 mdrun_mpi If I look at %CPU column, it is actually 100/(no. of processes) Why is all the cpu not 100% utilised? Also if I compare my performance, it is significantly hampered. Please suggest me the way so that I can run one simulation on all available nodes, cores and threads. 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] some code for writing topologies
All, Below is some code I wrote a few years ago during my PhD. I started with a list of bonds in a file called 'bonds' and t he used this list to automatically create the lists of angled and proper dihedrals. I went on to edit this code to create a topology for entire polymers based on a single monomer which you can figure out for yourself if need be. The list of bonds was created by eye and the structure is important to ensure that the angles and dihedrals are found correctly. The list was structured so that I started with the first atom in the gro file, looked at all atoms it was bonded to and then moved on the atom number 2. I did not count bonds where the atom bonded to this 'atom of interest' had a lower number than this 'atom of interest'. e.g. if atom 1 is bonded to atoms 2, 3, and 4 the first 3 entries in the bonds list read: 1 2 1 3 1 4 If atom 2 is bonded to atoms 1, 5 and 6 then there are only two entries for this atom: 2 5 2 6 This avoids having the same bond counted twice and it is essential that double counting of bonds is avoided. Note that if the molecule already has a sensible structure (i.e. bonds and angles are not too small or too large) then you could easily write some code to find the list of bonds for you, just specify that a bond occurs anywhere where two atoms are below a certain distance apart. I hope this helps some of you with your topologies. I realise that there are some tools already available for this but none of them worked for the polymers I was modelling. I imagine I am not the only one to have had this problem. Here is the code:-- program topol implicit none integer,parameter:: totalbonds = 603 integer,parameter:: atoms =514 !number of atoms in molecule integer,parameter:: maxbond=4 !max no of bonds per atom integer:: i,j,k,n !do loops integer:: iatom(totalbonds), jatom(totalbonds) !bond list integer:: ia(atoms,maxbond+1), ja, ka(maxbond+1) !angles integer:: id, jd, kd, ld integer:: count=0 !counts the number of bonds for an atom integer:: atombonds(atoms) !list of the number of bonds for each atom open(10,file='bonds') do i=1,totalbonds read(10,*) iatom(i), jatom(i) !print*,iatom(i), jatom(i) end do ia(:,:)=0 open(20,file='topology') !angles ! this takes the list of bonds which has been read in and finds two bonds that ! form and angle ijk. Essentially it looks through each atom in turn, finds all the ! atoms that are bonded to it and stores then in the array ia(:,:). ! This array or list is then used to construct the list of angles ijk. write(20,*)' ' write(20,*) '[ angles ]' do ja=1,atoms !atom at centre of angle count=0 !counter for number of bonds, this is reset for each atom ! ka(:)=0 do i=1,totalbonds!loop to find all atoms in the bond list bonded to atom ja if(iatom(i)==ja)then !look through first bond list count=count+1 print*, count, ja, jatom(i)!prints out to screen so the user can check it ia(ja,count)=jatom(i) end if if(jatom(i)==ja)then !look through second bond list count=count+1 print*,count, ja, iatom(i) !prints out to screen so the user can check it ia(ja,count)=iatom(i) end if end do !i loop , bonded atoms atombonds(ja)=count !add the count of bonds to the bonds list print*, ja, count, ' ::ia:', ia(ja,1:count) !prints out as a check if the program should stall if(count==2) then!write the angles to the topology file, if there are only two atoms bonded to atom j then there is only one angle write(20,*)ia(ja,1), ja, ia(ja,2) print*,' ',ia(ja,1), ja, ia(ja,2) else if(count.ge.3) then !if there are 3 or more atoms bonded to atom j then there are multiple angles do i=1,count do k=1,count if(k.le.i)cycle write(20,*)ia(ja,i),ja,ia(ja,k) print*,' ',ia(ja,i),ja,ia(ja,k) end do end do end if print*, '---' end do !ja loop !dihedrals ! this uses the list of angles ia(:,:) found above to construct the list of dihedral angles. ! It looks through the original bond list that was read in and finds how many angles (or bonds) ! are created about each atom at the end of each bond. This information is then used to construct ! a list of dihedral angles ijkl where j and k are form the original bond from the bonds list. write(20,*) ' ' write(20,*) '[ dihedrals ]' !ia(atoms,maxcount) records each atom that is bonded to a given atom !atombonds(atoms) records the number of bonds
Re: [gmx-users] parallel simulation
Hi, Is it a local work station or cluster with multiple CPUs? Which gromacs version did you install? On Mon, Oct 7, 2013 at 1:55 PM, pratibha kapoor kapoorpratib...@gmail.comwrote: I would like to run one simulation in parallel so that it utilises all the available nodes and cores. For that, I have compiled gromacs with mpi enabled and also installed openmpi on my machine. I am using the following command: mpirun -np 4 mdrun_mpi -v -s *.tpr When i use top command, I get: PID USER PR NI VIRT RES SHR S %CPU %MEMTIME+ COMMAND 22449 root 20 0 107m 59m 3152 R25 2.9 0:05.42 mdrun_mpi 22450 root 20 0 107m 59m 3152 R25 2.9 0:05.41 mdrun_mpi 22451 root 20 0 107m 59m 3152 R25 2.9 0:05.41 mdrun_mpi 22452 root 20 0 107m 59m 3152 R25 2.9 0:05.40 mdrun_mpi Similarly when i use mpirun -np 2 mdrun_mpi -v -s *.tpr, I get PID USER PR NI VIRT RES SHR S %CPU %MEMTIME+ COMMAND 22461 root 20 0 108m 59m 3248 R 50 3.0 5:58.64 mdrun_mpi 22462 root 20 0 108m 59m 3248 R 50 3.0 5:58.56 mdrun_mpi If I look at %CPU column, it is actually 100/(no. of processes) Why is all the cpu not 100% utilised? Also if I compare my performance, it is significantly hampered. Please suggest me the way so that I can run one simulation on all available nodes, cores and threads. 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 -- With Best Wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 -- 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] Bilayer thickness
Hi, I have used Grid-Mat program for calculating bilayer thickness and area per lipid for POPC bilayer. For bilayer thickness, without peptide, it provides the lateral area of system in angstrom sq. and also APL. (keeping APL as no) I separately calculated the APL with peptide, It also provides the lateral area of system and APL.(keeping thickness as no) which lateral area has to be considered as the thickness of the bilayer in terms of nm? both have different values. I am confused. which values should be reported for thickness and APL? Please help me. -- Archana Sonawani-Jagtap Senior Research Fellow, Biomedical Informatics Centre, NIRRH (ICMR), Parel Mumbai, India. 9960791339 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Bilayer thickness
On 10/7/13 8:00 AM, Archana Sonawani-Jagtap wrote: Hi, I have used Grid-Mat program for calculating bilayer thickness and area per lipid for POPC bilayer. For bilayer thickness, without peptide, it provides the lateral area of system in angstrom sq. and also APL. (keeping APL as no) I separately calculated the APL with peptide, It also provides the lateral area of system and APL.(keeping thickness as no) which lateral area has to be considered as the thickness of the bilayer in terms of nm? both have different values. I am confused. Lateral area and thickness are different concepts, so I'm not sure what your question is. The thickness values are mostly for plotting purposes, though you can average them and get a results reasonably similar to what you would get with g_dist. The APL values are reported individually for every lipid in the output file and the average ± std dev is printed to the screen. In the absence of your actual input files and the output produced, there's not much else I can offer to help. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] OPLS/AA + TIP5P, anybody?
Dear Chris, Thank you for your message. I uploaded everything to the redmine. I will let you know how the simulation with generated velocities went. I asked the authors about any exemplary input that worked with tip5p and oplsaa, but I did not get anything... Best, Grzegorz On 2013-10-04 17:20, Christopher Neale wrote: Dear Grzegorz: From a quick look at your .mdp, I also suggest that you go back to your system including the peptide that you had managed to finish EM with modified flexible tip5p but then crashed with the standard rigid tip5p during MD and try the MD again using gen-vel = yes if you're still seeing problems, why not upload your water-only system and your with-small-peptide test system to redmine. It's meant as a place to start a discussion, share files, and help us not to foget about a problem that may exist, so I am not sure why you hesitate. Also, you said that the authors of that other OPLS-Tip5p paper had no problems. You might ask them for .gro .mdp and .top files so that you can see exactly what they did and how it differs from what you are doing. Chris. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: parallel simulation
To add : I am running simulations on institute cluster with 8 nodes (2 cores each). Please suggest me the way so that I can run one simulation on all available nodes, cores and threads. Thanks in advance. On Mon, Oct 7, 2013 at 1:55 PM, pratibha kapoor kapoorpratib...@gmail.comwrote: I would like to run one simulation in parallel so that it utilises all the available nodes and cores. For that, I have compiled gromacs with mpi enabled and also installed openmpi on my machine. I am using the following command: mpirun -np 4 mdrun_mpi -v -s *.tpr When i use top command, I get: PID USER PR NI VIRT RES SHR S %CPU %MEMTIME+ COMMAND 22449 root 20 0 107m 59m 3152 R25 2.9 0:05.42 mdrun_mpi 22450 root 20 0 107m 59m 3152 R25 2.9 0:05.41 mdrun_mpi 22451 root 20 0 107m 59m 3152 R25 2.9 0:05.41 mdrun_mpi 22452 root 20 0 107m 59m 3152 R25 2.9 0:05.40 mdrun_mpi Similarly when i use mpirun -np 2 mdrun_mpi -v -s *.tpr, I get PID USER PR NI VIRT RES SHR S %CPU %MEMTIME+ COMMAND 22461 root 20 0 108m 59m 3248 R 50 3.0 5:58.64 mdrun_mpi 22462 root 20 0 108m 59m 3248 R 50 3.0 5:58.56 mdrun_mpi If I look at %CPU column, it is actually 100/(no. of processes) Why is all the cpu not 100% utilised? Also if I compare my performance, it is significantly hampered. Please suggest me the way so that I can run one simulation on all available nodes, cores and threads. 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] Calculating the distance between protein and ligand during ligand diffusion out of the box
Hello All, I have calculated the distance between the binding pocket of protein and the ligand molecule but due to ligand diffusion out of box, I am getting wrong distance as first it increases till 5nm and then decrease again to around 1nm during the simulation (which is not possible). I have fitted my trajectory with using trjconv -pbc mol -ur compact -center (protein) option. I have also tried the -nojump option but getting the same results for distances. Please suggest how to get the real distance without the PBC effect. -- *--- Thanks and Regards, Bipin Singh* -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Calculating the distance between protein and ligand during ligand diffusion out of the box
On 10/7/13 10:46 AM, bipin singh wrote: Hello All, I have calculated the distance between the binding pocket of protein and the ligand molecule but due to ligand diffusion out of box, I am getting wrong distance as first it increases till 5nm and then decrease again to around 1nm during the simulation (which is not possible). I have fitted my trajectory with using trjconv -pbc mol -ur compact -center (protein) option. I have also tried the -nojump option but getting the same results for distances. Please suggest how to get the real distance without the PBC effect. It sounds like that very well could be the real distance. If the ligand diffused out, it simply becomes part of the solvent around the protein and can diffuse around freely. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] Re: parallel simulation
You need to contact your cluster administrator for instructions of how to submit jobs to the cluster. Usually you have to create some kind of shell-script that specifies various parameters of your job and then submit it to a queue system. Below you submitted the job most likely to the 'head-node', the node you login first to work the cluster. Andreas -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users- boun...@gromacs.org] On Behalf Of pratibha kapoor Sent: 07 October 2013 14:46 To: gmx-users@gromacs.org Subject: [gmx-users] Re: parallel simulation To add : I am running simulations on institute cluster with 8 nodes (2 cores each). Please suggest me the way so that I can run one simulation on all available nodes, cores and threads. Thanks in advance. On Mon, Oct 7, 2013 at 1:55 PM, pratibha kapoor kapoorpratib...@gmail.comwrote: I would like to run one simulation in parallel so that it utilises all the available nodes and cores. For that, I have compiled gromacs with mpi enabled and also installed openmpi on my machine. I am using the following command: mpirun -np 4 mdrun_mpi -v -s *.tpr When i use top command, I get: PID USER PR NI VIRT RES SHR S %CPU %MEMTIME+ COMMAND 22449 root 20 0 107m 59m 3152 R25 2.9 0:05.42 mdrun_mpi 22450 root 20 0 107m 59m 3152 R25 2.9 0:05.41 mdrun_mpi 22451 root 20 0 107m 59m 3152 R25 2.9 0:05.41 mdrun_mpi 22452 root 20 0 107m 59m 3152 R25 2.9 0:05.40 mdrun_mpi Similarly when i use mpirun -np 2 mdrun_mpi -v -s *.tpr, I get PID USER PR NI VIRT RES SHR S %CPU %MEMTIME+ COMMAND 22461 root 20 0 108m 59m 3248 R 50 3.0 5:58.64 mdrun_mpi 22462 root 20 0 108m 59m 3248 R 50 3.0 5:58.56 mdrun_mpi If I look at %CPU column, it is actually 100/(no. of processes) Why is all the cpu not 100% utilised? Also if I compare my performance, it is significantly hampered. Please suggest me the way so that I can run one simulation on all available nodes, cores and threads. 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 mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Calculating the distance between protein and ligand during ligand diffusion out of the box
Thanks for the reply Dr. Justin. I have also thinking of the same possibility but to further confirm, I am sending the link for the plot of the distance between the COM of ligand binding pocket and COM of ligand molecule, please find some time to have a look at the plot and let me know if it seems a feasible behaviour during a simulation. http://researchweb.iiit.ac.in/~bipin.singh/plot.png On Mon, Oct 7, 2013 at 8:22 PM, Justin Lemkul jalem...@vt.edu wrote: On 10/7/13 10:46 AM, bipin singh wrote: Hello All, I have calculated the distance between the binding pocket of protein and the ligand molecule but due to ligand diffusion out of box, I am getting wrong distance as first it increases till 5nm and then decrease again to around 1nm during the simulation (which is not possible). I have fitted my trajectory with using trjconv -pbc mol -ur compact -center (protein) option. I have also tried the -nojump option but getting the same results for distances. Please suggest how to get the real distance without the PBC effect. It sounds like that very well could be the real distance. If the ligand diffused out, it simply becomes part of the solvent around the protein and can diffuse around freely. -Justin -- ==** Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.**edu jalem...@outerbanks.umaryland.edu | (410) 706-7441 ==** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- *--- Thanks and Regards, Bipin Singh* -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Calculating the distance between protein and ligand during ligand diffusion out of the box
On 10/7/13 1:39 PM, bipin singh wrote: Thanks for the reply Dr. Justin. I have also thinking of the same possibility but to further confirm, I am sending the link for the plot of the distance between the COM of ligand binding pocket and COM of ligand molecule, please find some time to have a look at the plot and let me know if it seems a feasible behaviour during a simulation. http://researchweb.iiit.ac.in/~bipin.singh/plot.png Looks like nothing more than random motion to me. Since you haven't told us what you're doing (unrestrained MD? pulling?), it's hard to comment further. -Justin On Mon, Oct 7, 2013 at 8:22 PM, Justin Lemkul jalem...@vt.edu wrote: On 10/7/13 10:46 AM, bipin singh wrote: Hello All, I have calculated the distance between the binding pocket of protein and the ligand molecule but due to ligand diffusion out of box, I am getting wrong distance as first it increases till 5nm and then decrease again to around 1nm during the simulation (which is not possible). I have fitted my trajectory with using trjconv -pbc mol -ur compact -center (protein) option. I have also tried the -nojump option but getting the same results for distances. Please suggest how to get the real distance without the PBC effect. It sounds like that very well could be the real distance. If the ligand diffused out, it simply becomes part of the solvent around the protein and can diffuse around freely. -Justin -- ==** Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.**edu jalem...@outerbanks.umaryland.edu | (410) 706-7441 ==** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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 takes phosphoserine as terminal ends
Hello Gromacs users, I want to obtain the topology file (topol.top) for this peptide Ace-Ser-Ser-Asp-Sep-Sep-Asp-Sep-Sep-Asp-Sep-Sep-Asp-Sep-Sep-Asp-NH2. I am using this ffG43a1p force field and this command pdb2gmx -f sereno2.pdb -o pep5-dpp-cap-linear-phospho_newbox_up_rotate.gro -ignh -ter -water spc I obtained the next error and warnings: Identified residue ACE1 as a starting terminus. Warning: Residue SEP5 in chain has different type (Other) from starting residue ACE1 (Protein). Warning: Residue SEP6 in chain has different type (Other) from starting residue ACE1 (Protein). Warning: Residue ASP7 in chain has different type (Protein) from starting residue ACE1 (Protein). Warning: Residue SEP8 in chain has different type (Other) from starting residue ACE1 (Protein). Warning: Residue SEP9 in chain has different type (Other) from starting residue ACE1 (Protein). More than 5 unidentified residues at end of chain - disabling further warnings. Program pdb2gmx, VERSION 4.5.3 Source code file: pdb2top.c, line: 1021 Fatal error: There is a dangling bond at at least one of the terminal ends. Select a proper terminal entry. According to my pdb file (www.dropbox.com/s/kihycqde78wy787/sereno2.pdb) my peptide is a continuous. I do not know how to figure out this mistake. I will appreciate if someone give me a hint. Thank you in advance, Eduardo - Eduardo Villarreal Ramírez Postdoctoral Research Fellow Mineralized Tissue Laboratory, Hospital for Special Surgery. -- View this message in context: http://gromacs.5086.x6.nabble.com/pdb2gmx-takes-phosphoserine-as-terminal-ends-tp5011684.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] pdb2gmx takes phosphoserine as terminal ends
On 10/7/13 4:40 PM, Villarealed wrote: Hello Gromacs users, I want to obtain the topology file (topol.top) for this peptide Ace-Ser-Ser-Asp-Sep-Sep-Asp-Sep-Sep-Asp-Sep-Sep-Asp-Sep-Sep-Asp-NH2. I am using this ffG43a1p force field and this command pdb2gmx -f sereno2.pdb -o pep5-dpp-cap-linear-phospho_newbox_up_rotate.gro -ignh -ter -water spc I obtained the next error and warnings: Identified residue ACE1 as a starting terminus. Warning: Residue SEP5 in chain has different type (Other) from starting residue ACE1 (Protein). Warning: Residue SEP6 in chain has different type (Other) from starting residue ACE1 (Protein). Warning: Residue ASP7 in chain has different type (Protein) from starting residue ACE1 (Protein). Warning: Residue SEP8 in chain has different type (Other) from starting residue ACE1 (Protein). Warning: Residue SEP9 in chain has different type (Other) from starting residue ACE1 (Protein). More than 5 unidentified residues at end of chain - disabling further warnings. Program pdb2gmx, VERSION 4.5.3 Source code file: pdb2top.c, line: 1021 Fatal error: There is a dangling bond at at least one of the terminal ends. Select a proper terminal entry. According to my pdb file (www.dropbox.com/s/kihycqde78wy787/sereno2.pdb) my peptide is a continuous. I do not know how to figure out this mistake. I will appreciate if someone give me a hint. You skipped step 5 in http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field#Adding_a_new_residue. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: pdb2gmx takes phosphoserine as terminal ends
Dear Justin, Your are right, as usual. Thank you so much. - Eduardo Villarreal Ramírez Postdoctoral Research Fellow Mineralized Tissue Laboratory, Hospital for Special Surgery. -- View this message in context: http://gromacs.5086.x6.nabble.com/pdb2gmx-takes-phosphoserine-as-terminal-ends-tp5011684p5011686.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Calculating the distance between protein and ligand during ligand diffusion out of the box
With a ligand diffusing as freely as I'm assuming (you've omitted a lot of info, box size etc.) you aren't going to get PBC to play nice, although -nojump should have atleast given you a different wrong answer. Centering the system on the same point you are using to define the binding pocket (may require custom index groups) should get you something more reasonable looking. Also, it depends on the size of your protein and what you're doing but you should consider if it's even relevant whether the ligand is 2nm away or 5? -Trayder On Tue, Oct 8, 2013 at 6:53 AM, Justin Lemkul jalem...@vt.edu wrote: On 10/7/13 1:39 PM, bipin singh wrote: Thanks for the reply Dr. Justin. I have also thinking of the same possibility but to further confirm, I am sending the link for the plot of the distance between the COM of ligand binding pocket and COM of ligand molecule, please find some time to have a look at the plot and let me know if it seems a feasible behaviour during a simulation. http://researchweb.iiit.ac.in/**~bipin.singh/plot.pnghttp://researchweb.iiit.ac.in/~bipin.singh/plot.png Looks like nothing more than random motion to me. Since you haven't told us what you're doing (unrestrained MD? pulling?), it's hard to comment further. -Justin On Mon, Oct 7, 2013 at 8:22 PM, Justin Lemkul jalem...@vt.edu wrote: On 10/7/13 10:46 AM, bipin singh wrote: Hello All, I have calculated the distance between the binding pocket of protein and the ligand molecule but due to ligand diffusion out of box, I am getting wrong distance as first it increases till 5nm and then decrease again to around 1nm during the simulation (which is not possible). I have fitted my trajectory with using trjconv -pbc mol -ur compact -center (protein) option. I have also tried the -nojump option but getting the same results for distances. Please suggest how to get the real distance without the PBC effect. It sounds like that very well could be the real distance. If the ligand diffused out, it simply becomes part of the solvent around the protein and can diffuse around freely. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.edu jalemkul@outerbanks.** umaryland.edu jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-usershttp://lists.gromacs.org/**mailman/listinfo/gmx-users htt**p://lists.gromacs.org/mailman/**listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchh**ttp://www.gromacs.org/Support/** Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Listshttp://www.gromacs.org/**Support/Mailing_Lists http://**www.gromacs.org/Support/**Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- ==** Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.**edu jalem...@outerbanks.umaryland.edu | (410) 706-7441 ==** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Can I generate Pulf files after mD running?
Dear gmx-users, I have just finished umbrella MD but I missed to type pullf/pullx options on mdrun. So, can I get pullf/pullx .xvg files from mdrun results? Best regards, Yoochan -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Regarding lipid bilayer
Dear All, I am trying to follow lipid bilayer simulation tutorial,I am getting struck at energy minimization same step after generating system_inflated.gro file. I get the same error, Fatal error: Invalid line in system_inflated.gro for atom 6439: 25.67360 25.77400 6.59650 I checked my system_inflated.gro and system.gro files too, the number of atoms in the second line are 6538 and 17503 respectively. I cannot figure out this error. Please help me in fixing this issue. Regards, V.Hasthi Student -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Calculating the distance between protein and ligand during ligand diffusion out of the box
Thanks for the reply Dr. Trayder and Dr. Justin. I have performed unrestrained MD with a ligand bound protein having surface exposed binding pocket (link of the image attached for clarification). I have used a cubic box with vectors 6.432nm and the system size was 4.117 3.878 and 4.059 (in nm). http://researchweb.iiit.ac.in/~bipin.singh/snapshot.png My doubt is how to discriminate between a real ligand binding/unbinding process and the rebinding observed due to PBC effects (i.e. when ligand diffuses out the box and a subsequent another ligand comes and bind from the adjacent periodic image, which may seen as a rebinding event during distance calculation). On Tue, Oct 8, 2013 at 6:37 AM, Trayder Thomas trayder.tho...@monash.eduwrote: With a ligand diffusing as freely as I'm assuming (you've omitted a lot of info, box size etc.) you aren't going to get PBC to play nice, although -nojump should have atleast given you a different wrong answer. Centering the system on the same point you are using to define the binding pocket (may require custom index groups) should get you something more reasonable looking. Also, it depends on the size of your protein and what you're doing but you should consider if it's even relevant whether the ligand is 2nm away or 5? -Trayder On Tue, Oct 8, 2013 at 6:53 AM, Justin Lemkul jalem...@vt.edu wrote: On 10/7/13 1:39 PM, bipin singh wrote: Thanks for the reply Dr. Justin. I have also thinking of the same possibility but to further confirm, I am sending the link for the plot of the distance between the COM of ligand binding pocket and COM of ligand molecule, please find some time to have a look at the plot and let me know if it seems a feasible behaviour during a simulation. http://researchweb.iiit.ac.in/**~bipin.singh/plot.png http://researchweb.iiit.ac.in/~bipin.singh/plot.png Looks like nothing more than random motion to me. Since you haven't told us what you're doing (unrestrained MD? pulling?), it's hard to comment further. -Justin On Mon, Oct 7, 2013 at 8:22 PM, Justin Lemkul jalem...@vt.edu wrote: On 10/7/13 10:46 AM, bipin singh wrote: Hello All, I have calculated the distance between the binding pocket of protein and the ligand molecule but due to ligand diffusion out of box, I am getting wrong distance as first it increases till 5nm and then decrease again to around 1nm during the simulation (which is not possible). I have fitted my trajectory with using trjconv -pbc mol -ur compact -center (protein) option. I have also tried the -nojump option but getting the same results for distances. Please suggest how to get the real distance without the PBC effect. It sounds like that very well could be the real distance. If the ligand diffused out, it simply becomes part of the solvent around the protein and can diffuse around freely. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.edu jalemkul@outerbanks.** umaryland.edu jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users http://lists.gromacs.org/**mailman/listinfo/gmx-users htt**p://lists.gromacs.org/mailman/**listinfo/gmx-users http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchh**ttp://www.gromacs.org/Support/** Mailing_Lists/Search http://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists http://www.gromacs.org/**Support/Mailing_Lists http://**www.gromacs.org/Support/**Mailing_Lists http://www.gromacs.org/Support/Mailing_Lists -- ==** Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.**edu jalem...@outerbanks.umaryland.edu | (410) 706-7441 ==** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-users http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Search
