[gmx-users] On dihedral type for CHARMM
Hi everyone! I am currently studying CHARMM ff and I have a question on the functional type of the CHARMM dihedral. On the ffbonded.itp, the function type for CHARMM dihedrals is 9. However, this functional type is not listed on Table 5.5 of the manual. I read that there are 9 supported functional types for dihedrals. Am I correct to assume that func=9is for the CHARMM dihedrals. thanks-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] On dihedral type for CHARMM
On 10/04/2011 4:12 PM, Mr Bernard Ramos wrote: Hi everyone! I am currently studying CHARMM ff and I have a question on the functional type of the CHARMM dihedral. On the ffbonded.itp, the function type for CHARMM dihedrals is 9. However, this functional type is not listed on Table 5.5 of the manual. I read that there are 9 supported functional types for dihedrals. Am I correct to assume that func=9is for the CHARMM dihedrals. I suspect your manual version is not up-to-date. The latest manual release(s) have dihedral type 9 (which is the same as 1, but you can have multiple of them in a [dihedraltypes] section). Mark -- 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] Extending Simulation
Dear All I used the following commands accoring to Extending Simulation in gromacs/Documentation/how-tos/Extending Simulation to extend my simulation. I entered: tpbconv -s npt-1.tpr-extend 100 -o npt-1-extend.tpr nohup mpirun -np 4 mdrun -s npt-1-extend.tpr -cpi npt-1.cpt Ii run this command on a node with 4 cpu. the result was these files: confout.gro , state.cpt ,md.log , traj.trr ,state_prev.cpt ,ener.edr , #confout.gro.1# ,#confout.gro.2# ,#confout.gro.3# ,# ener.edr.1# ,#ener.edr.2# ,#md.log.1 #,#traj.trr.1# ,#traj.trr.2# , I extended 4 files on 4 distinct nodes! it is excellent,because the number of outputs was different, for example one node produced 3 md.log and 4 confout.gro ! The main question is: which one of the resulted outputs are the main result? on wich do I must analyse? thanks in advance for your ideas -- 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] Extending Simulation
On 10/04/2011 5:40 PM, mohsen ramezanpour wrote: Dear All I used the following commands accoring to Extending Simulation in gromacs/Documentation/how-tos/Extending Simulation to extend my simulation. I entered: tpbconv -s npt-1.tpr-extend 100 -o npt-1-extend.tpr nohup mpirun -np 4 mdrun -s npt-1-extend.tpr -cpi npt-1.cpt Ii run this command on a node with 4 cpu. the result was these files: confout.gro , state.cpt ,md.log , traj.trr ,state_prev.cpt ,ener.edr , #confout.gro.1# ,#confout.gro.2# ,#confout.gro.3# ,# ener.edr.1# ,#ener.edr.2# ,#md.log.1 #,#traj.trr.1# ,#traj.trr.2# , I extended 4 files on 4 distinct nodes! That's not the behaviour you were looking for. You've run the same .tpr four times, once on each CPU. This is because mdrun was not compiled with MPI. See the installation instructions. it is excellent,because the number of outputs was different, for example one node produced 3 md.log and 4 confout.gro ! The main question is: which one of the resulted outputs are the main result? on wich do I must analyse? They should all be equivalent, but not necessarily binary identical. Mark -- 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] NPT.mdp parameters NOTE
Dear Dr.Justin As you have noticed in your tutorials,It is better to use Nose-Hoover for tempreture in the NPT.mdp file. You have used tau-t = 0.1 in most of your md.mdp files for generating npt ensemble. When I use a npt file with these settings,there is a Note as following: sorry,i can't remember the exact messge but :it says it is better to use a tau_t 20 times of another quantity, in my work the quantity=0.01 When I made tau_t=0.2 there was not any Note! Can I ignore this Note?Is it safe continuing with the same tau_t=0.1 as you used? -- 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] Extending Simulation
Dear Dr.Mark On Sun, Apr 10, 2011 at 12:20 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 10/04/2011 5:40 PM, mohsen ramezanpour wrote: Dear All I used the following commands accoring to Extending Simulation in gromacs/Documentation/how-tos/Extending Simulation to extend my simulation. I entered: tpbconv -s npt-1.tpr-extend 100 -o npt-1-extend.tpr nohup mpirun -np 4 mdrun -s npt-1-extend.tpr -cpi npt-1.cpt Ii run this command on a node with 4 cpu. the result was these files: confout.gro , state.cpt ,md.log , traj.trr ,state_prev.cpt ,ener.edr , #confout.gro.1# ,#confout.gro.2# ,#confout.gro.3# ,# ener.edr.1# ,#ener.edr.2# ,#md.log.1 #,#traj.trr.1# ,#traj.trr.2# , I extended 4 files on 4 distinct nodes! That's not the behaviour you were looking for. You've run the same .tpr four times, once on each CPU. This is because mdrun was not compiled with MPI. See the installation instructions. I think I explained bad.let me explain it more: Suppose I entered the above commands on just one node(with 4 cpu) for npt-1.tpr (just one time I entered these commands) besides if you were right it would result the same outputs when I run it on different nodes with the same commands,please see below! it is excellent,because the number of outputs was different, for example one node produced 3 md.log and 4 confout.gro ! The main question is: which one of the resulted outputs are the main result? on wich do I must analyse? They should all be equivalent, but not necessarily binary identical. Actually I checked all of them,they are different,with different averages of quantities, and all of them show a final text that means the program finished succesfully! what do you think Dr.Mark? Thanks in advance for your reply Mark -- 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] Extending Simulation
On 10/04/2011 6:04 PM, mohsen ramezanpour wrote: Dear Dr.Mark On Sun, Apr 10, 2011 at 12:20 PM, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote: On 10/04/2011 5:40 PM, mohsen ramezanpour wrote: Dear All I used the following commands accoring to Extending Simulation in gromacs/Documentation/how-tos/Extending Simulation to extend my simulation. I entered: tpbconv -s npt-1.tpr-extend 100 -o npt-1-extend.tpr nohup mpirun -np 4 mdrun -s npt-1-extend.tpr -cpi npt-1.cpt Ii run this command on a node with 4 cpu. the result was these files: confout.gro , state.cpt ,md.log , traj.trr ,state_prev.cpt ,ener.edr , #confout.gro.1# ,#confout.gro.2# ,#confout.gro.3# ,# ener.edr.1# ,#ener.edr.2# ,#md.log.1 #,#traj.trr.1# ,#traj.trr.2# , I extended 4 files on 4 distinct nodes! That's not the behaviour you were looking for. You've run the same .tpr four times, once on each CPU. This is because mdrun was not compiled with MPI. See the installation instructions. I think I explained bad.let me explain it more: Suppose I entered the above commands on just one node(with 4 cpu) for npt-1.tpr (just one time I entered these commands) You seem to have used mpirun to run four different mdrun processes, each using the same .tpr, one on each cpu. You should be trying to run one mdrun_mpi using that .tpr, but all four cpus working on the same run. Look at the top few lines of your .log. That will tell you how many nodes mdrun thought it was running on. I think you will see NNODES=1. If so, don't use this mdrun with mpirun. besides if you were right it would result the same outputs when I run it on different nodes with the same commands,please see below! Not strictly true. See http://www.gromacs.org/Documentation/Terminology/Reproducibility it is excellent,because the number of outputs was different, for example one node produced 3 md.log and 4 confout.gro ! The main question is: which one of the resulted outputs are the main result? on wich do I must analyse? They should all be equivalent, but not necessarily binary identical. Actually I checked all of them,they are different,with different averages of quantities, and all of them show a final text that means the program finished succesfully! The averages being the same or different merely reflect whether your run was reproducible. Assuming there was no output files in your working directory to start with, you've run the same irreproducible run four times, because you're using a non-MPI mdrun. Mark -- 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] Extending Simulation
Dear Dr.Mark Thank you very much you are right I understood your mean exactly, On Sun, Apr 10, 2011 at 12:44 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 10/04/2011 6:04 PM, mohsen ramezanpour wrote: Dear Dr.Mark On Sun, Apr 10, 2011 at 12:20 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 10/04/2011 5:40 PM, mohsen ramezanpour wrote: Dear All I used the following commands accoring to Extending Simulation in gromacs/Documentation/how-tos/Extending Simulation to extend my simulation. I entered: tpbconv -s npt-1.tpr-extend 100 -o npt-1-extend.tpr nohup mpirun -np 4 mdrun -s npt-1-extend.tpr -cpi npt-1.cpt Ii run this command on a node with 4 cpu. the result was these files: confout.gro , state.cpt ,md.log , traj.trr ,state_prev.cpt ,ener.edr , #confout.gro.1# ,#confout.gro.2# ,#confout.gro.3# ,# ener.edr.1# ,#ener.edr.2# ,#md.log.1 #,#traj.trr.1# ,#traj.trr.2# , I extended 4 files on 4 distinct nodes! That's not the behaviour you were looking for. You've run the same .tpr four times, once on each CPU. This is because mdrun was not compiled with MPI. See the installation instructions. I think I explained bad.let me explain it more: Suppose I entered the above commands on just one node(with 4 cpu) for npt-1.tpr (just one time I entered these commands) You seem to have used mpirun to run four different mdrun processes, each using the same .tpr, one on each cpu. You should be trying to run one mdrun_mpi using that .tpr, but all four cpus working on the same run. Look at the top few lines of your .log. That will tell you how many nodes mdrun thought it was running on. I think you will see NNODES=1. If so, don't use this mdrun with mpirun. besides if you were right it would result the same outputs when I run it on different nodes with the same commands,please see below! Not strictly true. See http://www.gromacs.org/Documentation/Terminology/Reproducibility it is excellent,because the number of outputs was different, for example one node produced 3 md.log and 4 confout.gro ! The main question is: which one of the resulted outputs are the main result? on wich do I must analyse? They should all be equivalent, but not necessarily binary identical. Actually I checked all of them,they are different,with different averages of quantities, and all of them show a final text that means the program finished succesfully! The averages being the same or different merely reflect whether your run was reproducible. Assuming there was no output files in your working directory to start with, you've run the same irreproducible run four times, because you're using a non-MPI mdrun. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] converging value
Dear All How can I determine the converged value of a simulation? Because the pressure has big oscilations around it's converging value but it is difficult to determine that value. can everybody guide me? 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] Different g_sas values between AMBER, CHARMM and GROMOS ff for DPC
Thank you David, My micelle simulated with the GROMOS ff slightly differs (size and shape) from the two others micelles, so i expected that the values total SAS value slightly differ. In case of the headgroup, they are located in the micelle interface region, so the SAS in case of the micelle simulated with GROMOS should be not so different (36 % less) than the others micelles You said that In order for g_sas to work with gromos force field one would have to increase the radius of the carbon atoms. For the 54 atoms the default value will be used. How to do that ? and for all the carbon atoms (including the headgroup carbon atoms). Thank you SA On 2011-04-09 19.06, sa wrote: Dear All, I have simulated three DPC micelles with the same size (54 lipids) with different force fields (CHARMM, AMBER et GROMOS53A6) and computed the average accessible surface areas for each lipids with g_sas (gmx4.5.3) I obtain the three average values for total DPC, the headgroup (phosphocholine) and the alkyl tail. Total (A2)Head Tail GROMOS53A6158.4 ± 4.8 54.8 ± 3.4 103.2 ± 3.8 AMBER 248.2 ± 8.7 76.2 ± 5.1 172.5 ± 5.2 CHARMM 242.7 ± 7.7 70.4 ± 4.1 172.4 ± 4.8 As you can see the ASA values are close between the micelles simulated with the CHARMM and AMBER ff, but larger than the values obtained from the micelle simulated with GROMOS ff especially for the headgroup. I am aware that CHARMM and AMBER are explicits ff whereas GROMOS is an united ff It is the reason I obtain a smaller values for GROMOS compared to two others ones ? Does g_sas tool take into account this. I have also noted when I use g_sas i obtain the following message WARNING: masses and atomic (Van der Waals) radii will be determined based on residue and atom names. These numbers can deviate from the correct mass and radius of the atom type. WARNING: could not find a Van der Waals radius for 54 atoms It is important ? Given your observations above, don't you think it might be? In order for g_sas to work with gromos force field one would have to increase the radius of the carbon atoms. For the 54 atoms the default value will be used. Thank you in advance for your advices. SA -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- 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] Different g_sas values between AMBER, CHARMM and GROMOS ff for DPC
On 2011-04-10 11.11, sa wrote: Thank you David, My micelle simulated with the GROMOS ff slightly differs (size and shape) from the two others micelles, so i expected that the values total SAS value slightly differ. In case of the headgroup, they are located in the micelle interface region, so the SAS in case of the micelle simulated with GROMOS should be not so different (36 % less) than the others micelles You said that In order for g_sas to work with gromos force field one would have to increase the radius of the carbon atoms. For the 54 atoms the default value will be used. How to do that ? and for all the carbon atoms (including the headgroup carbon atoms). edit vdwradii.dat. Then be careful to use an atom name that is specific for the FF such that your Amber and Charmm runs keep the correct value. Thank you SA On 2011-04-09 19.06, sa wrote: Dear All, I have simulated three DPC micelles with the same size (54 lipids) with different force fields (CHARMM, AMBER et GROMOS53A6) and computed the average accessible surface areas for each lipids with g_sas (gmx4.5.3) I obtain the three average values for total DPC, the headgroup (phosphocholine) and the alkyl tail. Total (A2)Head Tail GROMOS53A6158.4 ± 4.8 54.8 ± 3.4 103.2 ± 3.8 AMBER 248.2 ± 8.7 76.2 ± 5.1 172.5 ± 5.2 CHARMM 242.7 ± 7.7 70.4 ± 4.1 172.4 ± 4.8 As you can see the ASA values are close between the micelles simulated with the CHARMM and AMBER ff, but larger than the values obtained from the micelle simulated with GROMOS ff especially for the headgroup. I am aware that CHARMM and AMBER are explicits ff whereas GROMOS is an united ff It is the reason I obtain a smaller values for GROMOS compared to two others ones ? Does g_sas tool take into account this. I have also noted when I use g_sas i obtain the following message WARNING: masses and atomic (Van der Waals) radii will be determined based on residue and atom names. These numbers can deviate from the correct mass and radius of the atom type. WARNING: could not find a Van der Waals radius for 54 atoms It is important ? Given your observations above, don't you think it might be? In order for g_sas to work with gromos force field one would have to increase the radius of the carbon atoms. For the 54 atoms the default value will be used. Thank you in advance for your advices. SA -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.se mailto:sp...@xray.bmc.uu.se http://folding.bmc.uu.se -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- 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] NPT.mdp parameters NOTE
He told me you can use up to 0.5 in an off-list email and in fact, does so in the KALP-15 in DPPC example... On 2011-04-10 02:54:15AM -0500, mohsen ramezanpour wrote: Dear Dr.Justin As you have noticed in your tutorials,It is better to use Nose-Hoover for tempreture in the NPT.mdp file. You have used tau-t = 0.1 in most of your md.mdp files for generating npt ensemble. When I use a npt file with these settings,there is a Note as following: sorry,i can't remember the exact messge but :it says it is better to use a tau_t 20 times of another quantity, in my work the quantity=0.01 When I made tau_t=0.2 there was not any Note! Can I ignore this Note?Is it safe continuing with the same tau_t=0.1 as you used? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- === Peter C. Lai | University of Alabama-Birmingham Programmer/Analyst | BEC 257 Genetics, Div. of Research | 1150 10th Avenue South p...@uab.edu | Birmingham AL 35294-4461 (205) 690-0808 | === -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] converging value
On 10/04/2011 6:48 PM, mohsen ramezanpour wrote: Dear All How can I determine the converged value of a simulation? Because the pressure has big oscilations around it's converging value but it is difficult to determine that value. Longer simulations on bigger systems. Mark -- 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] Dangling bond error for dna
majid hasan wrote: Sorry, the pdb file is bigger than 50k so it won't attach, so its pasted below. Output of pdb2gmx is attached. You have numerous problems with this .pdb file: 1. All residues are listed as being the 3' end form. Your chain should start with a 5' end, include the middle residues, and end with a 3' form. 2. 5' ends do not have phosphate on them, per force field convention. 3. You have various incorrect atoms, and some incorrect atom names. Please refer to the dna.rtp file for your chosen force field to understand its expectations. Then you will need to manually fix your .pdb file by renaming, replacing, or removing whatever is in conflict. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] probelm of using amber force field
Dear GMX users, I have a question about running MD simulation using amber force field. It is easy to prepare the top and gro files of protein with amber force field, but how should I prepare the itp and gro files of small molecules with GAFF force field? I know the program ANTECHAMBER and tleap can generate the some molecule's topology and coordinate. Could someone give me some hints? Thanks very much in advance! -- Best wishes, Qinghua Liao Ph.D student of Tianjin University, China-- 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] probelm of using amber force field
fancy2012 wrote: Dear GMX users, I have a question about running MD simulation using amber force field. It is easy to prepare the top and gro files of protein with amber force field, but how should I prepare the itp and gro files of small molecules with GAFF force field? I know the program ANTECHAMBER and tleap can generate the some molecule's topology and coordinate. Could someone give me some hints? Thanks very much in advance! http://code.google.com/p/acpype/ is one common approach. -Justin -- _Best wishes,_ _Qinghua Liao_ _Ph.D student of Tianjin University, China_ -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] converging value
Dear Dr.Mark thank you for your attention How long is enough? for example I have run 200 ps for making npt(p=1 bar) for my system (300 nm^3) But the pressure is oscilating so much,and I can't be sure if it has converged or not! of course its average is approximately 5 bar (at the end of log file) Do you have any idea? I know it is not any problem if a quantity is oscilating around it's converged value. thanks in advance for your reply On Sun, Apr 10, 2011 at 3:09 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 10/04/2011 6:48 PM, mohsen ramezanpour wrote: Dear All How can I determine the converged value of a simulation? Because the pressure has big oscilations around it's converging value but it is difficult to determine that value. Longer simulations on bigger systems. Mark -- 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] converging value
On 10/04/2011 9:41 PM, mohsen ramezanpour wrote: Dear Dr.Mark thank you for your attention How long is enough? For example, when the size of error estimate reported by g_energy is smaller than the quantity you are trying to observe. That might take many nanoseconds in the case of observables based on fluctuations of atomic positions. There've been lots of mailing list threads on this topic. Mark for example I have run 200 ps for making npt(p=1 bar) for my system (300 nm^3) But the pressure is oscilating so much,and I can't be sure if it has converged or not! of course its average is approximately 5 bar (at the end of log file) Do you have any idea? I know it is not any problem if a quantity is oscilating around it's converged value. thanks in advance for your reply On Sun, Apr 10, 2011 at 3:09 PM, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote: On 10/04/2011 6:48 PM, mohsen ramezanpour wrote: Dear All How can I determine the converged value of a simulation? Because the pressure has big oscilations around it's converging value but it is difficult to determine that value. Longer simulations on bigger systems. Mark -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto: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] Error while performing a REMD simulation
2011/4/10 Mark Abraham mark.abra...@anu.edu.au: On 10/04/2011 11:44 AM, Justin A. Lemkul wrote: Maybe this is unrelated to the underlying problem, but hopefully it helps in the long run. Nothing worse than a reviewer saying, Nice project, but 100% of the data are junk. Bad idea, and 100% of the data are junk ? :-) Well, in this case you're not going to be scooped -while in the first case you have wasted your time AND someone else will redo your project (correctly) while you wait for your paper review to come back. m. -- 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] Error while performing a REMD simulation
2011/4/10 Mark Abraham mark.abra...@anu.edu.au: On 10/04/2011 10:58 AM, devicerandom wrote: A polite request for correct behaviour is suitable. Use of ALL CAPS is also a breach of netiquette. :-) Ouch. I just wanted to convey strength, it's not like I WROTE ALL THE MAIL IN ALL CAPS :-) However, will remember it next time. thanks, m. -- 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] converging value
You need to look at the dependence of the statistical value (in this case the average pressure) with (a) increasing equilibration time that you discard prior to collecting pressure data, and (b) increasing production simulation time that you include in your average. Create the first plot, and discard any data in the early part of the simulation for which there appears to be a drift (the discarded data will not be used in the second plot). Then create the second plot, where you should see large oscillations about an average value and these oscillations should get smaller as the simulation time is increased. You can gauge the remaining error by block averaging or (much better) comparing with another simulation that you ran. There are also other statistical methods available, but I prefer the simplicity of these. If your question is simply that you did these things but the oscillations remain large and you want to know how to get a more precise value, then the answer is simply to simulate longer. Chris. -- original message -- Dear All How can I determine the converged value of a simulation? Because the pressure has big oscilations around it's converging value but it is difficult to determine that value. can everybody guide me? Thanks in advance -- next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gm -- 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:gmx-users Digest, Vol 84, Issue 81
-- Message: 4 Date: Sun, 10 Apr 2011 18:55:15 +0800 (CST) From: fancy2012 fancy2...@yeah.net Subject: [gmx-users] probelm of using amber force field To: gmx-users gmx-users@gromacs.org Message-ID: 3ec402b.63dd.12f3f0d1e61.coremail.fancy2...@yeah.net Content-Type: text/plain; charset=gbk Dear GMX users, I have a question about running MD simulation using amber force field. It is easy to prepare the top and gro files of protein with amber force field, but how should I prepare the itp and gro files of small molecules with GAFF force field? I know the program ANTECHAMBER and tleap can generate the some molecule's topology and coordinate. Could someone give me some hints? Thanks very much in advance! -- Best wishes, Qinghua Liao Ph.D student of Tianjin University, China -- next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20110410/b7b8202b/attachment-0001.html -- Message: 5 Date: Sun, 10 Apr 2011 07:32:13 -0400 From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] probelm of using amber force field To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4da1953d.7060...@vt.edu Content-Type: text/plain; charset=x-gbk; format=flowed fancy2012 wrote: Dear GMX users, I have a question about running MD simulation using amber force field. It is easy to prepare the top and gro files of protein with amber force field, but how should I prepare the itp and gro files of small molecules with GAFF force field? I know the program ANTECHAMBER and tleap can generate the some molecule's topology and coordinate. Could someone give me some hints? Thanks very much in advance! http://code.google.com/p/acpype/ is one common approach. -Justin -- _Best wishes,_ _Qinghua Liao_ _Ph.D student of Tianjin University, China_ -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- Message: 6 Date: Sun, 10 Apr 2011 16:11:28 +0430 From: mohsen ramezanpour ramezanpour.moh...@gmail.com Subject: Re: [gmx-users] converging value To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: banlktimnexpd1mujgf4b9zjai4_rm_m...@mail.gmail.com Content-Type: text/plain; charset=iso-8859-1 Dear Dr.Mark thank you for your attention How long is enough? for example I have run 200 ps for making npt(p=1 bar) for my system (300 nm^3) But the pressure is oscilating so much,and I can't be sure if it has converged or not! of course its average is approximately 5 bar (at the end of log file) Do you have any idea? I know it is not any problem if a quantity is oscilating around it's converged value. thanks in advance for your reply On Sun, Apr 10, 2011 at 3:09 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 10/04/2011 6:48 PM, mohsen ramezanpour wrote: Dear All How can I determine the converged value of a simulation? Because the pressure has big oscilations around it's converging value but it is difficult to determine that value. Longer simulations on bigger systems. Mark -- 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 -- next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20110410/d6cde97e/attachment-0001.html -- Message: 7 Date: Sun, 10 Apr 2011 21:57:12 +1000 From: Mark Abraham mark.abra...@anu.edu.au Subject: Re: [gmx-users] converging value To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4da19b18.2030...@anu.edu.au Content-Type: text/plain; charset=iso-8859-1 On 10/04/2011 9:41 PM, mohsen ramezanpour wrote: Dear Dr.Mark thank you for your attention How long is enough? For example, when the size of error estimate reported by g_energy is smaller than the quantity you are trying to observe. That might take many nanoseconds in the case of observables based on fluctuations of atomic positions. There've been lots of mailing list threads on this topic. Mark for example I have run 200 ps for making npt(p=1 bar) for my system (300 nm^3) But the pressure is oscilating so much,and I can't be sure if it has converged or not! of course its average is approximately 5 bar (at the end of log file) Do you have any idea? I know it is not any problem if a quantity
Re: [gmx-users] Dangling bond error for dna
Okay, thank you. I'll try to fix it. Majid From: Justin A. Lemkul jalem...@vt.edu To: Gromacs Users' List gmx-users@gromacs.org Sent: Sun, April 10, 2011 4:17:59 AM Subject: Re: [gmx-users] Dangling bond error for dna majid hasan wrote: Sorry, the pdb file is bigger than 50k so it won't attach, so its pasted below. Output of pdb2gmx is attached. You have numerous problems with this .pdb file: 1. All residues are listed as being the 3' end form. Your chain should start with a 5' end, include the middle residues, and end with a 3' form. 2. 5' ends do not have phosphate on them, per force field convention. 3. You have various incorrect atoms, and some incorrect atom names. Please refer to the dna.rtp file for your chosen force field to understand its expectations. Then you will need to manually fix your .pdb file by renaming, replacing, or removing whatever is in conflict. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users 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] Different g_sas values between AMBER, CHARMM and GROMOS ff for DPC
Thank you David A bientôt SA -- Message: 1 Date: Sun, 10 Apr 2011 11:17:15 +0200 From: David van der Spoel sp...@xray.bmc.uu.se Subject: Re: [gmx-users] Different g_sas values between AMBER, CHARMM and GROMOS ff for DPC To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4da1759b.2000...@xray.bmc.uu.se Content-Type: text/plain; charset=ISO-8859-1; format=flowed On 2011-04-10 11.11, sa wrote: Thank you David, My micelle simulated with the GROMOS ff slightly differs (size and shape) from the two others micelles, so i expected that the values total SAS value slightly differ. In case of the headgroup, they are located in the micelle interface region, so the SAS in case of the micelle simulated with GROMOS should be not so different (36 % less) than the others micelles You said that In order for g_sas to work with gromos force field one would have to increase the radius of the carbon atoms. For the 54 atoms the default value will be used. How to do that ? and for all the carbon atoms (including the headgroup carbon atoms). edit vdwradii.dat. Then be careful to use an atom name that is specific for the FF such that your Amber and Charmm runs keep the correct value. Thank you SA On 2011-04-09 19.06, sa wrote: Dear All, I have simulated three DPC micelles with the same size (54 lipids) with different force fields (CHARMM, AMBER et GROMOS53A6) and computed the average accessible surface areas for each lipids with g_sas (gmx4.5.3) I obtain the three average values for total DPC, the headgroup (phosphocholine) and the alkyl tail. Total (A2)Head Tail GROMOS53A6158.4 ± 4.8 54.8 ± 3.4 103.2 ± 3.8 AMBER 248.2 ± 8.7 76.2 ± 5.1 172.5 ± 5.2 CHARMM 242.7 ± 7.7 70.4 ± 4.1 172.4 ± 4.8 As you can see the ASA values are close between the micelles simulated with the CHARMM and AMBER ff, but larger than the values obtained from the micelle simulated with GROMOS ff especially for the headgroup. I am aware that CHARMM and AMBER are explicits ff whereas GROMOS is an united ff It is the reason I obtain a smaller values for GROMOS compared to two others ones ? Does g_sas tool take into account this. I have also noted when I use g_sas i obtain the following message WARNING: masses and atomic (Van der Waals) radii will be determined based on residue and atom names. These numbers can deviate from the correct mass and radius of the atom type. WARNING: could not find a Van der Waals radius for 54 atoms It is important ? Given your observations above, don't you think it might be? In order for g_sas to work with gromos force field one would have to increase the radius of the carbon atoms. For the 54 atoms the default value will be used. Thank you in advance for your advices. SA -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.se mailto:sp...@xray.bmc.uu.se http://folding.bmc.uu.se -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! End of gmx-users Digest, Vol 84, Issue 80 * -- 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] Dangling bond error for dna
Is there any software that generates .pdb file consistent with amber forcefield requirements? I tried 3DNA, and GABEDIT, but 3DNA doesn't name residues in correct format i.e DX, and gabedit names every residue as DX3. Thanks, Majid From: Justin A. Lemkul jalem...@vt.edu To: Gromacs Users' List gmx-users@gromacs.org Sent: Sun, April 10, 2011 4:17:59 AM Subject: Re: [gmx-users] Dangling bond error for dna majid hasan wrote: Sorry, the pdb file is bigger than 50k so it won't attach, so its pasted below. Output of pdb2gmx is attached. You have numerous problems with this .pdb file: 1. All residues are listed as being the 3' end form. Your chain should start with a 5' end, include the middle residues, and end with a 3' form. 2. 5' ends do not have phosphate on them, per force field convention. 3. You have various incorrect atoms, and some incorrect atom names. Please refer to the dna.rtp file for your chosen force field to understand its expectations. Then you will need to manually fix your .pdb file by renaming, replacing, or removing whatever is in conflict. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users 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] Dangling bond error for dna
Okay, I am trying AmberTools as well. Thanks Justin! Majid From: Justin A. Lemkul jalem...@vt.edu To: Gromacs Users' List gmx-users@gromacs.org Sent: Sun, April 10, 2011 10:16:57 AM Subject: Re: [gmx-users] Dangling bond error for dna majid hasan wrote: Is there any software that generates .pdb file consistent with amber forcefield requirements? I tried 3DNA, and GABEDIT, but 3DNA doesn't name residues in correct format i.e DX, and gabedit names every residue as DX3. Perhaps xleap (part of AmberTools), but if your input has a bunch of incorrect atoms, I don't know how well it deals with replacing them. I seem to remember that it just writes new atoms and doesn't necessarily clean up the old ones, but my memory could be incorrect or the program may have been improved since last I tried it. http://ambermd.org/#AmberTools -Justin Thanks, Majid *From:* Justin A. Lemkul jalem...@vt.edu *To:* Gromacs Users' List gmx-users@gromacs.org *Sent:* Sun, April 10, 2011 4:17:59 AM *Subject:* Re: [gmx-users] Dangling bond error for dna majid hasan wrote: Sorry, the pdb file is bigger than 50k so it won't attach, so its pasted below. Output of pdb2gmx is attached. You have numerous problems with this .pdb file: 1. All residues are listed as being the 3' end form. Your chain should start with a 5' end, include the middle residues, and end with a 3' form. 2. 5' ends do not have phosphate on them, per force field convention. 3. You have various incorrect atoms, and some incorrect atom names. Please refer to the dna.rtp file for your chosen force field to understand its expectations. Then you will need to manually fix your .pdb file by renaming, replacing, or removing whatever is in conflict. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.eduhttp://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users 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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users 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] the gmx-4.5.4 can not be compiled but the gmx-4.5.3 can
Dear gmxers, I have had tried to install gmx-4.5.4 by compiling the source code. The first step ./configure finished without any error, but the second step running make reported some errors as follows /usr/lib64/gcc/x86_64-suse-linux/4.4/../../../../x86_64-suse-linux/bin/ld: /usr/local/lib/libfftw3f.a(tensor.o): relocation R_X86_64_32 against `a local symbol' can not be used when making a shared object; recompile with -fPIC /usr/local/lib/libfftw3f.a: could not read symbols: Bad value collect2: ld returned 1 exit status make[3]: *** [libmd.la] Error 1 make[3]: Leaving directory `/root/Download/gromacs-4.5.4/src/mdlib' make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory `/root/Download/gromacs-4.5.4/src' make[1]: *** [all] Error 2 make[1]: Leaving directory `/root/Download/gromacs-4.5.4/src' make: *** [all-recursive] Error 1 Note that I can install successfully gmx-4.5.3 using the very same procedure. How to deal with this problem? Please give me some hints. Thanks a lot. Yours sincerely, Chaofu Wu, Dr.-- 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] the gmx-4.5.4 can not be compiled but the gmx-4.5.3 can
Dear gmxers, I have had tried to install gmx-4.5.4 by compiling the source code. The first step ./configure finished without any error, but the second step running make reported some errors as follows /usr/lib64/gcc/x86_64-suse-linux/4.4/../../../../x86_64-suse-linux/bin/ld: /usr/local/lib/libfftw3f.a(tensor.o): relocation R_X86_64_32 against `a local symbol' can not be used when making a shared object; recompile with -fPIC /usr/local/lib/libfftw3f.a: could not read symbols: Bad value collect2: ld returned 1 exit status make[3]: *** [libmd.la] Error 1 make[3]: Leaving directory `/root/Download/gromacs-4.5.4/src/mdlib' make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory `/root/Download/gromacs-4.5.4/src' make[1]: *** [all] Error 2 make[1]: Leaving directory `/root/Download/gromacs-4.5.4/src' make: *** [all-recursive] Error 1 Note that I can install successfully gmx-4.5.3 using the very same procedure. How to deal with this problem? Please give me some hints. Thanks a lot. The list archive deal with this issue several times, as do the installation instructions on the web page. Mark -- 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] mdrun segmentation fault
Hello gmx users, My system for NVT equilbration runs into segmentation fault as soon as I try to run it. It does not give any warning or hint of what might be going wrong. Since I am a new user I am having difficulty exploring the plausible reasons. System: Protein( polyhistidine), 20 2,5-dihydroxybenzoic acid anions, 1:1 water: methanol (~3000 molecules of each) in 8 nm cube I had had EM of the system using steepest decent. Outcome: Steepest Descents converged to machine precision in 15 steps, but did not reach the requested Fmax 1000. Potential Energy = 1.5354981e+19 Maximum force =inf on atom 651 Norm of force =inf *The minim.mdp *is: ; minim.mdp - used as input into grompp to generate em.tpr ; Parameters describing what to do, when to stop and what to save integrator = steep ; Algorithm (steep = steepest descent minimization) emtol= 1000.0; Stop minimization when the maximum force 1000.0 kJ/mol/nm emstep = 0.02 ; Energy step size nsteps = 5 ; Maximum number of (minimization) steps to perform ; 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= 1.0; Cut-off for making neighbor list (short range forces) coulombtype = PME; Treatment of long range electrostatic interactions rcoulomb = 1.0; Short-range electrostatic cut-off rvdw = 1.0; Short-range Van der Waals cut-off pbc = xyz ; Periodic Boundary Conditions (yes/no) constraints = none *The nvt.mdp*: title= hist NVT equilibration define = -DPOSRES ; position restrain the protein ; Run parameters integrator = md ; leap-frog integrator nsteps = 5 ; 2 * 5 = 100 ps dt= 0.002 ; 2 fs ; Output control nstxout = 100; save coordinates every 0.2 ps nstvout = 100; save velocities every 0.2 ps nstenergy = 100; save energies every 0.2 ps nstlog = 100; update log file every 0.2 ps ; Bond parameters continuation = no ; first dynamics run constraint_algorithm = lincs ; holonomic constraints constraints = none ; lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighborsearching ns_type = grid ; search neighboring grid cells nstlist = 5 ; 10 fs rlist= 1.0; short-range neighborlist cutoff (in nm) rcoulomb = 1.0; short-range electrostatic cutoff (in nm) rvdw = 1.0; 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 ; modified Berendsen thermostat tc-grps = Protein Non-Protein ; two coupling groups - more accurate tau_t= 0.1 0.1 ; time constant, in ps ref_t= 300300 ; reference temperature, one for each group, in K ; Pressure coupling is off pcoupl = no ; no pressure coupling in NVT ; Periodic boundary conditions pbc = xyz; 3-D PBC ; Dispersion correction DispCorr = EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = yes; assign velocities from Maxwell distribution gen_temp = 300; temperature for Maxwell distribution gen_seed = -1 ; generate a random seed I tried to decrease the step size, that also runs into seg fault error. Kindly guide. Thanks, SN -- 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] comm-grps for a membrane-protein-ligand system
Should I couple a ligand associated with a membrane protein to the same COM group as the Protein_POPC group? It makes sense to me that would be the case since if we are investigating the interaction between protein+membrane and ligand we want to have the same COM correction vector applied to both relative to SOL_Ions but I just wanted to make sure... -- === Peter C. Lai | University of Alabama-Birmingham Programmer/Analyst | BEC 257 Genetics, Div. of Research | 1150 10th Avenue South p...@uab.edu | Birmingham AL 35294-4461 (205) 690-0808 | === -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] mdrun segmentation fault
Hello gmx users, My system for NVT equilbration runs into segmentation fault as soon as I try to run it. It does not give any warning or hint of what might be going wrong. Since I am a new user I am having difficulty exploring the plausible reasons. System: Protein( polyhistidine), 20 2,5-dihydroxybenzoic acid anions, 1:1 water: methanol (~3000 molecules of each) in 8 nm cube I had had EM of the system using steepest decent. Outcome: Steepest Descents converged to machine precision in 15 steps, but did not reach the requested Fmax 1000. Potential Energy = 1.5354981e+19 Maximum force =inf on atom 651 Norm of force =inf So that's broken already - you have enormous positive energy and infinite forces. Stop there and fix it. Either your starting configuration has severe atomic overlaps (go and visualize it with the periodic box), or some of your topology is broken (try a box of methanol on its own, try the protein in vacuum, try a single acid in vacuum) Mark *The minim.mdp *is: ; minim.mdp - used as input into grompp to generate em.tpr ; Parameters describing what to do, when to stop and what to save integrator = steep ; Algorithm (steep = steepest descent minimization) emtol= 1000.0; Stop minimization when the maximum force 1000.0 kJ/mol/nm emstep = 0.02 ; Energy step size nsteps = 5 ; Maximum number of (minimization) steps to perform ; 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= 1.0; Cut-off for making neighbor list (short range forces) coulombtype = PME; Treatment of long range electrostatic interactions rcoulomb = 1.0; Short-range electrostatic cut-off rvdw = 1.0; Short-range Van der Waals cut-off pbc = xyz ; Periodic Boundary Conditions (yes/no) constraints = none *The nvt.mdp*: title= hist NVT equilibration define = -DPOSRES ; position restrain the protein ; Run parameters integrator = md ; leap-frog integrator nsteps = 5 ; 2 * 5 = 100 ps dt= 0.002 ; 2 fs ; Output control nstxout = 100; save coordinates every 0.2 ps nstvout = 100; save velocities every 0.2 ps nstenergy = 100; save energies every 0.2 ps nstlog = 100; update log file every 0.2 ps ; Bond parameters continuation = no ; first dynamics run constraint_algorithm = lincs ; holonomic constraints constraints = none ; lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighborsearching ns_type = grid ; search neighboring grid cells nstlist = 5 ; 10 fs rlist= 1.0; short-range neighborlist cutoff (in nm) rcoulomb = 1.0; short-range electrostatic cutoff (in nm) rvdw = 1.0; 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 ; modified Berendsen thermostat tc-grps = Protein Non-Protein ; two coupling groups - more accurate tau_t= 0.1 0.1 ; time constant, in ps ref_t= 300300 ; reference temperature, one for each group, in K ; Pressure coupling is off pcoupl = no ; no pressure coupling in NVT ; Periodic boundary conditions pbc = xyz; 3-D PBC ; Dispersion correction DispCorr = EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = yes; assign velocities from Maxwell distribution gen_temp = 300; temperature for Maxwell distribution gen_seed = -1 ; generate a random seed I tried to decrease the step size, that also runs into seg fault error. Kindly guide. Thanks, SN -- 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] 1,5 and 1,6 LJ interactions for OPLS AA SEI
Hi everyone! The OPLS AA SEI for carbohydrates scales the 1,5 and 1,6 interaction by a certain factor. How do I go about introducing the scaling of these intearctions in the ff parameters? The CHARMM ff also has certain 1,4 parameters, I am not sure how we can go about placing these specific parameters in the ff. Your help is greatly appreciated. Thanks. See use of fudgeQQ and nrexcl in section 5.7.1, and discussion of pairs and exclusions in 5.3.4 and 5.4. Basically you will want to exclude 1,5 and 1,6 interactions with nrexcl and generate pair parameters by some mechanism. Different scalings for 1,4 1,5 and 1,6 would be a pain. Mark -- 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
