Re: [gmx-users] QMMM
Good luck. I followed the instructions and was not successful. On Tue, Mar 8, 2011 at 12:48 AM, Haresh ajanihar...@gmail.com wrote: Hello everyone, I want install gromacs with mopac7 for qmmm. Can you guide me for installation procedure Thank you. -- 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] GPU GROMACS
Is anyone working on a build GROMACS with CUDA other than the OpenMM project? I would like to build this with explicit solvents and as I understand it, OpenMM is implicit. -- Jack http://drugdiscoveryathome.com http://hydrogenathome.org -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] Checkpointing
We have mdrun integrated into our distributed computing project. When your users suspend or close the manger it checkpoints, so when they open again it continues mdrun where it left off. However, when users reboot, it starts from the beginning. We are using this command line to execute the work. mdrun.exe (-v -x -c -o md.pdb -e -cpo md.next -cpi md.cpt -deffnm md) I have a seperate checkpoint for output so after this simulation we can extend the workunit. Should we try using this append option? Checkpoints containing the complete state of the system are written at regular intervals (option -cpt) to the file -cpo, unless option -cpt is set to -1. A simulation can be continued by reading the full state from file with option -cpi. This option is intelligent in the way that if no checkpoint file is found, Gromacs just assumes a normal run and starts from the first step of the tpr file. With checkpointing you can also use the option -append to just continue writing to the previous output files. This is not enabled by default since it is potentially dangerous if you move files, but if you just leave all your files in place and restart mdrun with exactly the same command (with options -cpi and -append) the result will be the same as from a single run. The contents will be binary identical (unless you use dynamic load balancing), but for technical reasons there might be some extra energy frames when using checkpointing (necessary for restarts without appending). -- Jack http://drugdiscoveryathome.com http://hydrogenathome.org -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] Checkpointing
I will try it without the checkpointing flags. If that fails, maybe I'll introduce some python into this integration. Check if the checkpoint already exists. On Tue, Feb 2, 2010 at 6:18 PM, Mark Abraham mark.abra...@anu.edu.au wrote: - Original Message - From: Jack Shultz j...@drugdiscoveryathome.com Date: Wednesday, February 3, 2010 2:36 Subject: [gmx-users] Checkpointing To: Discussion list for GROMACS users gmx-users@gromacs.org, Andrey Voronkov a...@drugdiscoveryathome.com We have mdrun integrated into our distributed computing project. When your users suspend or close the manger it checkpoints, so when they open again it continues mdrun where it left off. However, when users reboot, it starts from the beginning. We are using this command line to execute the work. mdrun.exe (-v -x -c -o md.pdb -e -cpo md.next -cpi md.cpt - deffnm md) If you're using this input line always, then you're getting what you're asking for - an mdrun that begins from the state in md.cpt. Since you're never updating that, it doesn't change. Try not stipulating different -cpo and -cpi and see what the native coping mechanism is. Otherwise, you'll have to write a bunch of scripting logic to decide which .cpt to use each restart. Mark I have a seperate checkpoint for output so after this simulation we can extend the workunit. Should we try using this append option? Checkpoints containing the complete state of the system are written at regular intervals (option -cpt) to the file -cpo, unless option -cpt is set to -1. A simulation can be continued by reading the full state from file with option -cpi. This option is intelligent in the way that if no checkpoint file is found, Gromacs just assumes a normal run and starts from the first step of the tpr file. With checkpointing you can also use the option -append to just continue writing to the previous output files. This is not enabled by default since it is potentially dangerous if you move files, but if you just leave all your files in place and restart mdrun with exactly the same command (with options -cpi and -append) the result will be the same as from a single run. The contents will be binary identical (unless you use dynamic load balancing), but for technical reasons there might be some extra energy frames when using checkpointing (necessary for restarts without appending). -- Jack http://drugdiscoveryathome.com http://hydrogenathome.org -- gmx-users mailing list gmx-us...@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- gmx-users mailing list gmx-us...@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- Jack http://drugdiscoveryathome.com http://hydrogenathome.org -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] Checkpointing
So you mean something like -cpi state.cpt -cpo state.cpt ? If so, I'll try this approach again. I had a little trouble doing it this way previously. I think I had trouble with the extension scripts doing it this way. On Tue, Feb 2, 2010 at 11:56 PM, Mark Abraham mark.abra...@anu.edu.au wrote: On 03/02/10 15:44, Jack Shultz wrote: I will try it without the checkpointing flags. That's not quite what I said. I suggested not using *different* filenames for -cpo and -cpi. What you want is the output file from a former run to transparently become the input file for the subsequent one, and I expect GROMACS will handle this for you if you let it. Try some things and see. Mark If that fails, maybe I'll introduce some python into this integration. Check if the checkpoint already exists. On Tue, Feb 2, 2010 at 6:18 PM, Mark Abrahammark.abra...@anu.edu.au wrote: - Original Message - From: Jack Shultzj...@drugdiscoveryathome.com Date: Wednesday, February 3, 2010 2:36 Subject: [gmx-users] Checkpointing To: Discussion list for GROMACS usersgmx-users@gromacs.org, Andrey Voronkova...@drugdiscoveryathome.com We have mdrun integrated into our distributed computing project. When your users suspend or close the manger it checkpoints, so when they open again it continues mdrun where it left off. However, when users reboot, it starts from the beginning. We are using this command line to execute the work. mdrun.exe (-v -x -c -o md.pdb -e -cpo md.next -cpi md.cpt - deffnm md) If you're using this input line always, then you're getting what you're asking for - an mdrun that begins from the state in md.cpt. Since you're never updating that, it doesn't change. Try not stipulating different -cpo and -cpi and see what the native coping mechanism is. Otherwise, you'll have to write a bunch of scripting logic to decide which .cpt to use each restart. Mark I have a seperate checkpoint for output so after this simulation we can extend the workunit. Should we try using this append option? Checkpoints containing the complete state of the system are written at regular intervals (option -cpt) to the file -cpo, unless option -cpt is set to -1. A simulation can be continued by reading the full state from file with option -cpi. This option is intelligent in the way that if no checkpoint file is found, Gromacs just assumes a normal run and starts from the first step of the tpr file. With checkpointing you can also use the option -append to just continue writing to the previous output files. This is not enabled by default since it is potentially dangerous if you move files, but if you just leave all your files in place and restart mdrun with exactly the same command (with options -cpi and -append) the result will be the same as from a single run. The contents will be binary identical (unless you use dynamic load balancing), but for technical reasons there might be some extra energy frames when using checkpointing (necessary for restarts without appending). -- Jack http://drugdiscoveryathome.com http://hydrogenathome.org -- gmx-users mailing list gmx-us...@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- gmx-users mailing list gmx-us...@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- gmx-users mailing list gmx-us...@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- Jack http://drugdiscoveryathome.com http://hydrogenathome.org -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] Re: including a custom itp file in topology
I confess I don't know the difference between rtp and itp. What I was hoping was an easier way to generate topologies for complexes that have non-standard residue names like LIG. Alan's acpypi works. You just have to do some extra scripting. But it seems like pdb2gmx should have a way to load the files describing the non-standard residue names directly. On Fri, Jan 29, 2010 at 6:24 AM, Alan alanwil...@gmail.com wrote: Dear Berk, I beg your pardon, but I have to assume that what you wrote below is not correct so, right? Should it be 'ligand.rtp' instead of 'ligand.itp'? Once I have my hands on this new pdb2gmx, I believe I can tweak acpypi to generate rtp files as well (but hdb and else probably not). Cheers, Alan On Fri, Jan 29, 2010 at 11:00, gmx-users-requ...@gromacs.org wrote: of them. So you can just put, e.g., a file called ligand.itp in your force field or current dir and pdb2gmx will read it. -- Alan Wilter Sousa da Silva, D.Sc. PDBe group, PiMS project http://www.pims-lims.org/ EMBL - EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK +44 (0)1223 492 583 (office) -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- Jack http://drugdiscoveryathome.com http://hydrogenathome.org -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] including a custom itp file in topology
Hi, I was trying to figure out if there is a short-cut for what I'm doing. I have complexes that I'm trying to prep using pdb2gmx. The ligand does not have a standard residue name. The way I know this can work is seperating out the ligand and protein into seperate files and preping the ligand using acpypi and the protein using pdb2gmx. Then incorporating them into a single pdb complex and including a reference to the ligand.itp (generated by acpypi) into a complex topology file. Is there any shortcut to doing this? any way to reference the ligand's itp file when running pdb2gmx? -- Jack http://drugdiscoveryathome.com http://hydrogenathome.org -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] Missing Residues are list ind pdb file
I'm trying to prep Fe-Hydrogenase again (1YQW). I took out all the non-standard residues. Re-named n-terminal and c-terminal residues. Took out connects because that worked last time though I'm uncertain if connect really maters. Another issue with preping a protein. Its says I a missing H and HA for this residue, but have those atoms listed there. Why does it say CYSH instead of CYS2 on residue 15 ??? ffamber99sb.hdb does not list CYSH as a resdue. http://boinc.drugdiscoveryathome.com/protein.pdb.txt http://boinc.drugdiscoveryathome.com/pdb2gmx.txt ATOM 232 N CYS2 15 5.467 7.021 7.435 1.00 0.00 ATOM 233 H CYS2 15 6.122 7.731 7.139 1.00 0.00 ATOM 234 CA CYS2 15 5.957 5.650 7.604 1.00 0.00 ATOM 235 HA CYS2 15 5.114 4.975 7.752 1.00 0.00 ATOM 236 CB CYS2 15 6.737 5.195 6.365 1.00 0.00 ATOM 237 2HB CYS2 15 6.774 4.106 6.322 1.00 0.00 ATOM 238 3HB CYS2 15 6.264 5.578 5.461 1.00 0.00 ATOM 239 SG CYS2 15 8.466 5.762 6.309 1.00 0.00 ATOM 240 HG CYS2 15 8.764 5.185 5.148 1.00 0.00 ATOM 241 C CYS2 15 6.841 5.543 8.845 1.00 0.00 ATOM 242 O CYS2 15 7.324 4.457 9.169 1.00 0.00 WARNING: atom H is missing in residue CYSH 15 in the pdb file You might need to add atom H to the hydrogen database of residue CYSH in the file ff???.hdb (see the manual) WARNING: atom HA is missing in residue CYSH 15 in the pdb file You might need to add atom HA to the hydrogen database of residue CYSH in the file ff???.hdb (see the manual) WARNING: atom HB1 is missing in residue CYSH 15 in the pdb file You might need to add atom HB1 to the hydrogen database of residue CYSH in the file ff???.hdb (see the manual) WARNING: atom HB2 is missing in residue CYSH 15 in the pdb file You might need to add atom HB2 to the hydrogen database of residue CYSH in the file ff???.hdb (see the manual) -- Jack http://drugdiscoveryathome.com http://hydrogenathome.org -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] Unstable Minimizations
Problem Solved. I replaced HETATM with ATOM, I fixed BOTH N-terminal and C-terminal. I kept TER and END. Removed all CONECT. Renamed the CYS to CYS2. No other non-AminoAcid residues were present. Most of this is described by the FFAmber site http://chemistry.csulb.edu/ffamber/ 2) *(!) Residue Nomenclature:* Residues in the AMBER ports are named according to their position in the sequence (i.e. terminal, non-terminal, monomer) following standard AMBER conventions. For this reason, it may be necessary to rename residues in the .pdb file you will import beforehand. Please note that all residues are named in the residue topology files (i.e. ffamber*.rtp), so if you are unsure of the correct residue name to use, you should be able to find it there. The .rtp files are ordered as follows: water models (TIP), ions urea (URE), peptide terminal capping residues (ie. ACE, NH2, NMe), non-terminal amino acids (i.e. TYR, ALA), non-terminal acidic amino acids (i.e. ASH, GLH, etc.), C-terminal amino acids (i.e. CALA, CGLY), N-terminal amino acids (i.e. NALA, NGLY), and all nucleic acid residues. Nucleic acids listed at the end of each .rtp follow the following order for each residue type: DNA is first, followed by RNA, in the order 5'-term, 3'-term, non-terminal, and monomer. The three .pdb files above are examples of how pdb files shoud be modified. Residues in the ffamber ports have been named as follows: *(a)* *Non-terminal amino and nucleic acid residues* follow standard AMBER naming conventions. To avoid confusion between GROMACS and AMBER conventions, we have omitted the redundant HIS residue, leaving HID, HIE, HIP, and terminal versions of these topologies. Additionally, due to the automated changing of certain residue names by pdb2gmx, the LYS and CYS residues have been renamed LYP (Lysine plus) and CYN (Cysteine neutral, compared to AMBER residue CYM = Cysteine minus). *(b)* *C- and N-terminal amino acids* include a C or N prefix respectively, so C-terminal ALA is CALA and N-ternimal PHE is NPHE. As with non-terminal versions, the LYS and CYS terminal residues are listed as NLYP,CLYP and NCYN,CCYN. *(c)* *Nucleic acid residues* come in four flavors. All residue names include XY, where X = D or R for DNA or RNA respectively, and Y = first letter of the nucleotide name. A suffix (XY*Z*) is added for monomers (Z=N), 5'-terminal (Z=5), and 3'-terminal (Z=3) residues. For example, 3'-term DNA Cytosine = DC3, 5'-term RNA Cytosine = RC5, non-terminal DNA Cytosine = DC, and lone RNA Cytosine monomer = RCN. *(d)* *Cys disulfide bonds* can be instituted by changing the names of the CYS residues involved in the disulfide bonds to CYS2. On Mon, Jan 11, 2010 at 11:57 AM, Justin A. Lemkul jalem...@vt.edu wrote: Jack Shultz wrote: Well some of the problems in the log relate to unresolved exceptions processing the ligands, those ligands are skipped. But I should probably just test the receptors seperate from the workflow and merged ligands. I will check this list provided by Tsjerk. Possibly the numbering is off. Anyway its the structures that need a little work. 6. there should be no atoms in residues that are not listed in the building block entry, except possibly for hydrogen atoms, which can be stripped using the -ignh flag Currently I use -ignh, should I see what happens when I remove this option? Will that reveal innappropriate atoms that I should remove? Removing -ignh implies that all hydrogen atoms are present and named according to the specifics of the building blocks. It's not a useful diagnostic for missing or inappropriate atoms. What is of great concern (as Tsjerk pointed out) is the 3-nm bond identified by pdb2gmx. Is there a missing loop in the protein? -Justin On Sun, Jan 10, 2010 at 9:58 PM, Justin A. Lemkul jalem...@vt.edumailto: jalem...@vt.edu wrote: On 1/10/10 9:47 PM, Jack Shultz wrote: Thanks Justin, I went back to the original pdb files. These were conformations of the same protein derived from molecular dynamics simulations performed by Andrey. What I intially attempted was preping the structures using tleap, hoping to paint in missing atoms for residues. Then use this to replace Well, it seems that you may be hoping for too much :) Your log file shows a whole bunch of failures that look to be related to some early processing of your structure, and other warnings about close contacts detected in tleap. I think you may need to start with an actual intact structure, or else coax your preparation steps to make this happen. I am not too familiar with tleap and sleap, do they magically fix missing atoms? -Justin non-standard residues sed s/PRO\ A\ \ \ 1/NPROA\ \ \ 1/g fzd2_md7-8_c6_cc.pdb | sed s/PRO\ B\ \ \ 1/NPROB\ \ \ 1/g | sed s/PHE\ A\ \ 99/CPHEA\ \ 99/g | sed s/PHE\ B\ \ 99/CPHEB\ \ 99/g | sed s
Re: [gmx-users] Unstable Minimizations
Well some of the problems in the log relate to unresolved exceptions processing the ligands, those ligands are skipped. But I should probably just test the receptors seperate from the workflow and merged ligands. I will check this list provided by Tsjerk. Possibly the numbering is off. Anyway its the structures that need a little work. 6. there should be no atoms in residues that are not listed in the building block entry, except possibly for hydrogen atoms, which can be stripped using the -ignh flag Currently I use -ignh, should I see what happens when I remove this option? Will that reveal innappropriate atoms that I should remove? On Sun, Jan 10, 2010 at 9:58 PM, Justin A. Lemkul jalem...@vt.edu wrote: On 1/10/10 9:47 PM, Jack Shultz wrote: Thanks Justin, I went back to the original pdb files. These were conformations of the same protein derived from molecular dynamics simulations performed by Andrey. What I intially attempted was preping the structures using tleap, hoping to paint in missing atoms for residues. Then use this to replace Well, it seems that you may be hoping for too much :) Your log file shows a whole bunch of failures that look to be related to some early processing of your structure, and other warnings about close contacts detected in tleap. I think you may need to start with an actual intact structure, or else coax your preparation steps to make this happen. I am not too familiar with tleap and sleap, do they magically fix missing atoms? -Justin non-standard residues sed s/PRO\ A\ \ \ 1/NPROA\ \ \ 1/g fzd2_md7-8_c6_cc.pdb | sed s/PRO\ B\ \ \ 1/NPROB\ \ \ 1/g | sed s/PHE\ A\ \ 99/CPHEA\ \ 99/g | sed s/PHE\ B\ \ 99/CPHEB\ \ 99/g | sed s/O\ \ \ CPHE/OC1\ CPHE/g | sed s/OXT\ CPHE/OC2\ CPHE/g | sed s/HIS\ /HID\ /g | sed s/LYS\ /LYP\ /g | sed s/CYS\ /CYN\ /g protein2.pdb Then fixed the nterminal residue name. Finally replaced all CYS to CYS2 I went back and did the same thing except for tleap. It pdb2gmx seems to process these files without needing the tleap step. Still I see some of the same lincs errors. rms 10.669050, max 173.182678 (between atoms 1857 and 1859) rms 10.669803, max 173.177811 (between atoms 1857 and 1859) rms 10.670179, max 173.175400 (between atoms 1857 and 1859) rms 10.670368, max 173.174149 (between atoms 1857 and 1859) rms 10.670460, max 173.173553 (between atoms 1857 and 1859) rms 10.670508, max 173.173141 (between atoms 1857 and 1859) rms 10.670531, max 173.173035 (between atoms 1857 and 1859) rms 10.670543, max 173.172958 (between atoms 1857 and 1859) rms 10.670549, max 173.172928 (between atoms 1857 and 1859) rms 10.670552, max 173.172913 (between atoms 1857 and 1859) rms 10.670554, max 173.172913 (between atoms 1857 and 1859) rms 10.670554, max 173.172913 (between atoms 1857 and 1859) ATOM 1857 CA HIE 120 43.362 28.084 25.727 1.00 0.00 ATOM 1858 HA HIE 120 43.677 27.135 25.748 1.00 0.00 ATOM 1859 CB HIE 120 42.112 28.226 24.788 1.00 0.00 also this atom consistently has a very high Fmax Step=3, Dmax= 1.4e-02 nm, Epot= 1.45860e+10 Fmax= 2.82224e+12, atom= 19392 Step=4, Dmax= 7.2e-03 nm, Epot= 1.45396e+10 Fmax= 2.82207e+12, atom= 19392 Step=5, Dmax= 3.6e-03 nm, Epot= 1.45106e+10 Fmax= 2.82194e+12, atom= 19392 Step=6, Dmax= 1.8e-03 nm, Epot= 1.44953e+10 Fmax= 2.82181e+12, atom= 19392 Step=7, Dmax= 9.0e-04 nm, Epot= 1.44887e+10 Fmax= 2.82196e+12, atom= 19392 Step=8, Dmax= 4.5e-04 nm, Epot= 1.44850e+10 Fmax= 2.82196e+12, atom= 19392 Step=9, Dmax= 2.2e-04 nm, Epot= 1.44832e+10 Fmax= 2.82196e+12, atom= 19392 Step= 10, Dmax= 1.1e-04 nm, Epot= 1.44822e+10 Fmax= 2.82196e+12, atom= 19392 Step= 11, Dmax= 5.6e-05 nm, Epot= 1.44818e+10 Fmax= 2.82196e+12, atom= 19392 Step= 12, Dmax= 2.8e-05 nm, Epot= 1.44815e+10 Fmax= 2.82196e+12, atom= 19392 Step= 13, Dmax= 1.4e-05 nm, Epot= 1.44814e+10 Fmax= 2.82196e+12, atom= 19392 Its not clear to me what we should do to correct this structures...maybe Andrey has some input. http://boinc.drugdiscoveryathome.com/em_restrained_rcs_mdrun2.txt On Sun, Jan 10, 2010 at 5:37 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: On 1/10/10 5:18 PM, Jack Shultz wrote: I am trying to get this workflow opperational. However, my systems are getting unstable. I have preped two mdp files: 1) one for restrained 2) unrestrained. LINCS errors appear for restrained and unrestrained has infinite energy appearing. http://boinc.drugdiscoveryathome.com/_em_restrained_rcs_mdrun.txt_ http://boinc.drugdiscoveryathome.com/em_restrained_rcs_mdrun.txt __ This log file shows several long bond warnings, which may be the root of your problem. See here: http://www.gromacs.org/Documentation/Errors#Long_bonds_and.2for_missing_atoms Since your minimization is failing immediately
[gmx-users] Unstable Minimizations
I am trying to get this workflow opperational. However, my systems are getting unstable. I have preped two mdp files: 1) one for restrained 2) unrestrained. LINCS errors appear for restrained and unrestrained has infinite energy appearing. http://boinc.drugdiscoveryathome.com/*em_restrained_rcs_mdrun.txthttp://boinc.drugdiscoveryathome.com/em_restrained_rcs_mdrun.txt * ** This is where I get the LINCS Warnings Step -1, time -0.001 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.461520, max 14.428611 (between atoms 1668 and 1669) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length Steepest Descents: Tolerance (Fmax) = 1.0e+04 Number of steps= 100 Warning: 1-4 interaction between 1658 and 1672 at distance 2.655 which is larger than the 1-4 table size 2.400 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file or with user tables increase the table size Step=0, Dmax= 1.0e-02 nm, Epot= 1.09364e+09 Fmax= 2.21154e+11, atom= 3292 Step 1, time 0.001 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.680509, max 22.293625 (between atoms 1668 and 1670) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length What is a reasonable increase in table-extension. Is this a mis-leading suggestion? Here is the log from the unrestrained minimization. http://boinc.drugdiscoveryathome.com/*em_rcs_mdrun.txthttp://boinc.drugdiscoveryathome.com/em_rcs_mdrun.txt * Here is a zip archive containing the working directory for this minimization. Its about 428 kb http://boinc.drugdiscoveryathome.com/rcs_ga_run_10_bt_Fzd2-MD7-MD8-7.zip_lig_24205_ChemDiv_5754-2873_ts_1263004110202172000.zip -- Jack http://drugdiscoveryathome.com http://hydrogenathome.org -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] Unstable Minimizations
Thanks Justin, I went back to the original pdb files. These were conformations of the same protein derived from molecular dynamics simulations performed by Andrey. What I intially attempted was preping the structures using tleap, hoping to paint in missing atoms for residues. Then use this to replace non-standard residues sed s/PRO\ A\ \ \ 1/NPROA\ \ \ 1/g fzd2_md7-8_c6_cc.pdb | sed s/PRO\ B\ \ \ 1/NPROB\ \ \ 1/g | sed s/PHE\ A\ \ 99/CPHEA\ \ 99/g | sed s/PHE\ B\ \ 99/CPHEB\ \ 99/g | sed s/O\ \ \ CPHE/OC1\ CPHE/g | sed s/OXT\ CPHE/OC2\ CPHE/g | sed s/HIS\ /HID\ /g | sed s/LYS\ /LYP\ /g | sed s/CYS\ /CYN\ /g protein2.pdb Then fixed the nterminal residue name. Finally replaced all CYS to CYS2 I went back and did the same thing except for tleap. It pdb2gmx seems to process these files without needing the tleap step. Still I see some of the same lincs errors. rms 10.669050, max 173.182678 (between atoms 1857 and 1859) rms 10.669803, max 173.177811 (between atoms 1857 and 1859) rms 10.670179, max 173.175400 (between atoms 1857 and 1859) rms 10.670368, max 173.174149 (between atoms 1857 and 1859) rms 10.670460, max 173.173553 (between atoms 1857 and 1859) rms 10.670508, max 173.173141 (between atoms 1857 and 1859) rms 10.670531, max 173.173035 (between atoms 1857 and 1859) rms 10.670543, max 173.172958 (between atoms 1857 and 1859) rms 10.670549, max 173.172928 (between atoms 1857 and 1859) rms 10.670552, max 173.172913 (between atoms 1857 and 1859) rms 10.670554, max 173.172913 (between atoms 1857 and 1859) rms 10.670554, max 173.172913 (between atoms 1857 and 1859) ATOM 1857 CA HIE 120 43.362 28.084 25.727 1.00 0.00 ATOM 1858 HA HIE 120 43.677 27.135 25.748 1.00 0.00 ATOM 1859 CB HIE 120 42.112 28.226 24.788 1.00 0.00 also this atom consistently has a very high Fmax Step=3, Dmax= 1.4e-02 nm, Epot= 1.45860e+10 Fmax= 2.82224e+12, atom= 19392 Step=4, Dmax= 7.2e-03 nm, Epot= 1.45396e+10 Fmax= 2.82207e+12, atom= 19392 Step=5, Dmax= 3.6e-03 nm, Epot= 1.45106e+10 Fmax= 2.82194e+12, atom= 19392 Step=6, Dmax= 1.8e-03 nm, Epot= 1.44953e+10 Fmax= 2.82181e+12, atom= 19392 Step=7, Dmax= 9.0e-04 nm, Epot= 1.44887e+10 Fmax= 2.82196e+12, atom= 19392 Step=8, Dmax= 4.5e-04 nm, Epot= 1.44850e+10 Fmax= 2.82196e+12, atom= 19392 Step=9, Dmax= 2.2e-04 nm, Epot= 1.44832e+10 Fmax= 2.82196e+12, atom= 19392 Step= 10, Dmax= 1.1e-04 nm, Epot= 1.44822e+10 Fmax= 2.82196e+12, atom= 19392 Step= 11, Dmax= 5.6e-05 nm, Epot= 1.44818e+10 Fmax= 2.82196e+12, atom= 19392 Step= 12, Dmax= 2.8e-05 nm, Epot= 1.44815e+10 Fmax= 2.82196e+12, atom= 19392 Step= 13, Dmax= 1.4e-05 nm, Epot= 1.44814e+10 Fmax= 2.82196e+12, atom= 19392 Its not clear to me what we should do to correct this structures...maybe Andrey has some input. http://boinc.drugdiscoveryathome.com/em_restrained_rcs_mdrun2.txt On Sun, Jan 10, 2010 at 5:37 PM, Justin A. Lemkul jalem...@vt.edu wrote: On 1/10/10 5:18 PM, Jack Shultz wrote: I am trying to get this workflow opperational. However, my systems are getting unstable. I have preped two mdp files: 1) one for restrained 2) unrestrained. LINCS errors appear for restrained and unrestrained has infinite energy appearing. http://boinc.drugdiscoveryathome.com/_em_restrained_rcs_mdrun.txt_ http://boinc.drugdiscoveryathome.com/em_restrained_rcs_mdrun.txt __ This log file shows several long bond warnings, which may be the root of your problem. See here: http://www.gromacs.org/Documentation/Errors#Long_bonds_and.2for_missing_atoms Since your minimization is failing immediately, there is something physically unreasonable about your structure, such that EM cannot resolve the problem. Note, too, that one of the long bond warnings pertained to atom 1668, which is the location of the first LINCS warning. Coincidence? Not likely. Re-examine the starting structure and figure out if anything is missing or poorly reconstructed (e.g., from initially missing atoms). This is where I get the LINCS Warnings Step -1, time -0.001 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.461520, max 14.428611 (between atoms 1668 and 1669) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length Steepest Descents: Tolerance (Fmax) = 1.0e+04 Number of steps= 100 Warning: 1-4 interaction between 1658 and 1672 at distance 2.655 which is larger than the 1-4 table size 2.400 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file or with user tables increase the table size Step=0, Dmax= 1.0e-02 nm, Epot= 1.09364e+09 Fmax= 2.21154e+11, atom= 3292 Step 1, time 0.001 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.680509, max 22.293625 (between atoms 1668 and 1670) bonds that rotated more than 30 degrees: atom 1 atom 2
[gmx-users] Mopac integration with gromacs
I am trying to use one of the free versions of mopac. I read there are some problems with mopac 7 and mopac 6 gives better results. In any case I am having trouble compiling either one. Has anyone had success with it? -- Jack http://drugdiscoveryathome.com http://hydrogenathome.org -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] trouble minimizing structure with mdrun
It seemed to run in NAMD with or without the infamous Fe4S4 center gromacs with amber99SB or OPLSA with or without exotic species seems to fail. Eventually I want to figure out this QM/MM integration with MOPAC but that is a subject for later. Let me at least see if pure MM works. I noticed that the solvation box I created using GROMACS did not center the box on the protein. There was quite a big offset leave more than half the molecule exposed. VMD did however solvate it right on the center of mass. Even with the structure solvated, relaxed and ionized gromacs failed. Further effort I ran Zephyr which is a GUI integration with OpenMMGromacs. That uses amber96 and implicit solvent. The application seems to run, but I was not able to load any trajectories and obtain further data to analyze the results. On Mon, Jan 4, 2010 at 2:44 AM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Jack, Can you be more specific? A quick glance at 1YQW shows that there's quite a bit of exotic stuff, including several times the infamous Fe4S4 center. How did you deal with that? At first instance, what protocol did you used, and what error did you get (and at which point)? After preparation with (V|NA)MD, did pdb2gmx correctly assign chains, or did it tie chains together? In the latter case it would have issued a number of Long Bond Warnings. Did everything else odd show up in the output of any of those steps? Did you actually read through it? Cheers, Tsjerk On Mon, Jan 4, 2010 at 1:38 AM, Jack Shultz j...@drugdiscoveryathome.com wrote: I've been having trouble minimizing a structure using gromacs so I decided to try using another MD app and see if I can generate a more relaxed structure. Using VMD NAMD I was able to minimize and run MD for this structure from RCSB.ORG 1YQW.pdb. It was solvated and ionized. I then took the last frame from a 10,000 step trajectory and exported it into a pdb file. I preped it so it was compatible with amber99sb port for gromacs read it into tleap using amebr99sb and wrote a pdb file from that Then fixed residues so it it was compatible with gromac pdb2gmx -ff amber99sb -f protein2.pdb -water spce -ignh editconf -bt triclinic -f conf.gro -d 1.0 genbox -cp out.gro -cs ffamber_tip3p.gro grompp -f em.mdp echo 13 |genion -s topol.tpr -neutral -conc 0.15 -p topol.top grompp -f em.mdp -c out.gro mdrun -s topol.tpr -v Back Off! I just backed up md.log to ./#md.log.2# Getting Loaded... Reading file topol.tpr, VERSION 4.0.5 (single precision) Loaded with Money Back Off! I just backed up traj.trr to ./#traj.trr.2# Back Off! I just backed up ener.edr to ./#ener.edr.2# Polak-Ribiere Conjugate Gradients: Tolerance (Fmax) = 2.0e+02 Number of steps = 1 F-max = 2.97876e+06 on atom 16106 F-Norm = 2.59700e+04 Step 0, Epot=4.125301e+07, Fnorm=2.399e+04, Fmax=2.975e+06 (atom 16106) Step 1, Epot=4.111934e+07, Fnorm=2.285e+04, Fmax=2.969e+06 (atom 16106) Step 2, Epot=4.092903e+07, Fnorm=2.216e+04, Fmax=2.959e+06 (atom 16106) Step 127, Epot=7.765358e+06, Fnorm=1.020e+05, Fmax=2.836e+07 (atom 28298) Step 128, Epot=1.606771e+08, Fnorm=6.739e+07, Fmax=1.876e+10 (atom 10310) Step 129, Epot=5.454451e+09, Fnorm=4.339e+09, Fmax=1.179e+12 (atom 36500) There were 2 inconsistent shifts. Check your topology em.mdp parameters define = -DFLEXIBLE integrator = cg nsteps = 1 constraints = none emtol = 200.0 nstcgsteep = 10 ; do a steep every 10 steps of cg emstep = 0.01 ; used with steep nstcomm = 1 coulombtype = PME ns_type = grid rlist = 1.0 rcoulomb = 1.0 rvdw = 1.4 Tcoupl = no Pcoupl = no gen_vel = no nstxout = 0 ; write coords every # step optimize_fft = yes table-extension = 100 ld_seed = -1 -- Jack http://drugdiscoveryathome.com http://hydrogenathome.org -- gmx-users mailing list gmx-us...@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- Tsjerk A. Wassenaar, Ph.D. Computational Chemist Medicinal Chemist Neuropharmacologist -- gmx-users mailing list gmx-us...@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- Jack http://drugdiscoveryathome.com http://hydrogenathome.org -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests
Re: [gmx-users] Dead Link or Restricted Access to link
Thanks! On Mon, Jan 4, 2010 at 5:13 AM, zjxu z...@mail.shcnc.ac.cn wrote: Jack Shultz 写道: The links to the videos don't work on this page. Hybrid QM/MM simulations with GROMACS, QM/MM application (slides,video 1,video 2,video 3) - (Gerrit Groenhof). http://www.gromacs.org/Documentation/How-tos/QMMM Hi Jack, I will send this message to the one who is in charge of the videos. Maybe the link has been changed. Instead, the link http://www.dddc.ac.cn/embo04/index.htm point to the same videos , and it works for me. the videos: http://www.dddc.ac.cn/embo04/photo_dv.htm# good luck zjxu -- gmx-users mailing list gmx-us...@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- Jack http://drugdiscoveryathome.com http://hydrogenathome.org -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] trouble minimizing structure with mdrun
I did a little more checking on the structures, I notice the results from genion move part of the protein far outside the solvent box. I shall try this without the genion step I put all the files in the working directory for this preperation in a zip archive under http://boinc.drugdiscoveryathome.com/1YQW.zip On Mon, Jan 4, 2010 at 2:22 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Jack, On Mon, Jan 4, 2010 at 2:44 AM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Jack, snip After preparation with (V|NA)MD, did pdb2gmx correctly assign chains, or did it tie chains together? In the latter case it would have issued a number of Long Bond Warnings. Did anything else odd show up in the output of any of those steps? Did you actually read through it? Post pdb2gmx/grompp output to help us help you. Cheers, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. Computational Chemist Medicinal Chemist Neuropharmacologist -- gmx-users mailing list gmx-us...@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- Jack http://drugdiscoveryathome.com http://hydrogenathome.org -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] trouble minimizing structure with mdrun
maybe I should go directly from pdb2gmx to grompp seeing as I have already solvated and ionized the protein in VMD. On Mon, Jan 4, 2010 at 8:04 PM, Jack Shultz j...@drugdiscoveryathome.com wrote: I did a little more checking on the structures, I notice the results from genion move part of the protein far outside the solvent box. I shall try this without the genion step I put all the files in the working directory for this preperation in a zip archive under http://boinc.drugdiscoveryathome.com/1YQW.zip On Mon, Jan 4, 2010 at 2:22 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Jack, On Mon, Jan 4, 2010 at 2:44 AM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Jack, snip After preparation with (V|NA)MD, did pdb2gmx correctly assign chains, or did it tie chains together? In the latter case it would have issued a number of Long Bond Warnings. Did anything else odd show up in the output of any of those steps? Did you actually read through it? Post pdb2gmx/grompp output to help us help you. Cheers, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. Computational Chemist Medicinal Chemist Neuropharmacologist -- gmx-users mailing list gmx-us...@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- Jack http://drugdiscoveryathome.com http://hydrogenathome.org -- Jack http://drugdiscoveryathome.com http://hydrogenathome.org -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] Dead Link or Restricted Access to link
The links to the videos don't work on this page. Hybrid QM/MM simulations with GROMACS, QM/MM application (slides,video 1,video 2,video 3) - (Gerrit Groenhof). http://www.gromacs.org/Documentation/How-tos/QMMM -- Jack http://drugdiscoveryathome.com http://hydrogenathome.org -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] trouble minimizing structure with mdrun
I've been having trouble minimizing a structure using gromacs so I decided to try using another MD app and see if I can generate a more relaxed structure. Using VMD NAMD I was able to minimize and run MD for this structure from RCSB.ORG 1YQW.pdb. It was solvated and ionized. I then took the last frame from a 10,000 step trajectory and exported it into a pdb file. I preped it so it was compatible with amber99sb port for gromacs read it into tleap using amebr99sb and wrote a pdb file from that Then fixed residues so it it was compatible with gromac pdb2gmx -ff amber99sb -f protein2.pdb -water spce -ignh editconf -bt triclinic -f conf.gro -d 1.0 genbox -cp out.gro -cs ffamber_tip3p.gro grompp -f em.mdp echo 13 |genion -s topol.tpr -neutral -conc 0.15 -p topol.top grompp -f em.mdp -c out.gro mdrun -s topol.tpr -v Back Off! I just backed up md.log to ./#md.log.2# Getting Loaded... Reading file topol.tpr, VERSION 4.0.5 (single precision) Loaded with Money Back Off! I just backed up traj.trr to ./#traj.trr.2# Back Off! I just backed up ener.edr to ./#ener.edr.2# Polak-Ribiere Conjugate Gradients: Tolerance (Fmax) = 2.0e+02 Number of steps=1 F-max = 2.97876e+06 on atom 16106 F-Norm= 2.59700e+04 Step 0, Epot=4.125301e+07, Fnorm=2.399e+04, Fmax=2.975e+06 (atom 16106) Step 1, Epot=4.111934e+07, Fnorm=2.285e+04, Fmax=2.969e+06 (atom 16106) Step 2, Epot=4.092903e+07, Fnorm=2.216e+04, Fmax=2.959e+06 (atom 16106) Step 127, Epot=7.765358e+06, Fnorm=1.020e+05, Fmax=2.836e+07 (atom 28298) Step 128, Epot=1.606771e+08, Fnorm=6.739e+07, Fmax=1.876e+10 (atom 10310) Step 129, Epot=5.454451e+09, Fnorm=4.339e+09, Fmax=1.179e+12 (atom 36500) There were 2 inconsistent shifts. Check your topology em.mdp parameters define = -DFLEXIBLE integrator = cg nsteps = 1 constraints = none emtol = 200.0 nstcgsteep = 10 ; do a steep every 10 steps of cg emstep = 0.01 ; used with steep nstcomm = 1 coulombtype = PME ns_type = grid rlist = 1.0 rcoulomb = 1.0 rvdw = 1.4 Tcoupl = no Pcoupl = no gen_vel = no nstxout = 0 ; write coords every # step optimize_fft = yes table-extension = 100 ld_seed = -1 -- Jack http://drugdiscoveryathome.com http://hydrogenathome.org -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] tpr older version message
If I preped the tpr using amber forcefields, could that be the reason? The mdrun I am using does not have any force field libraries in its directory. On Sat, Dec 26, 2009 at 11:57 PM, Mark Abraham mark.abra...@anu.edu.au wrote: Jack Shultz wrote: I preped this ligand using acpypi followed by grompp grompp -f em.mdp -c ligand_GMX.gro -p ligand_GMX.top I tested this .tpr file on my server. WheI had another computer run it I get the following message. However we are using the same versions of gromacs. Back Off! I just backed up md.log to ./#md.log.2# --- Program mdrun, VERSION 4.0.5 Source code file: tpxio.c, line: 1643 Fatal error: Can not read file topol.tpr, this file is from a Gromacs version which is older than 2.0 Make a new one with grompp or use a gro or pdb file, if possible --- I'd say it's evident that if the file is not corrupted (use gmxcheck), the GROMACS installations weren't the same (unmodified) version. Reproduce the conditions and run grompp -h to inspect the version. Perhaps you are having a problem with a shared-library mismatch. If you have such an old version of GROMACS around, either uninstall it and retire the sysadmin, or send the computer to a museum :-) Mark -- gmx-users mailing list gmx-us...@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- Jack http://drugdiscoveryathome.com http://hydrogenathome.org -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] tpr older version message
Hi Marc, I figured it out. I tried upir suggestion and tested the gmxcheck but got the following errors gmxcheck.exe -s1 topol.tpr Please give me TWO run input (.tpr/.tpa/.tpb) files or specify the -m flag to generate a methods.tex file gmxcheck.exe -s1 topol.tpr -m --- Program gmxcheck, VERSION 4.0.5 Source code file: tpxio.c, line: 1643 Fatal error: Can not read file topol.tpr, this file is from a Gromacs version which is older than 2.0 Make a new one with grompp or use a gro or pdb file, if possible --- gcq#332: Thanx for Using GROMACS - Have a Nice Day But then decided I need to run the grompp on my clients along with the pre-processing libraries generated by acpypi. Then tested the mdrun on the .tpr this generated. Then it was missing the aminoacids.dat I downloaded it and everything seems to work. I will now make some additional steps on this workflow so this should now work! Thanks again for your help I very much appreciate it. On Sun, Dec 27, 2009 at 7:18 PM, Mark Abraham mark.abra...@anu.edu.au wrote: Jack Shultz wrote: If I preped the tpr using amber forcefields, could that be the reason? No. The mdrun I am using does not have any force field libraries in its directory. That's irrelevant. Only non-mdrun tools care about the contents of $GMXLIB or local force field files. The point of GROMPP is that it is the GROMacs Pre-Processor that does all such for mdrun. When you get some advice, it's good politics to be seen to follow those up (or reject with reasons) before casting about wildly with other theories :-) You don't want the people giving free advice feeling like you're wasting their time! Mark On Sat, Dec 26, 2009 at 11:57 PM, Mark Abraham mark.abra...@anu.edu.au wrote: Jack Shultz wrote: I preped this ligand using acpypi followed by grompp grompp -f em.mdp -c ligand_GMX.gro -p ligand_GMX.top I tested this .tpr file on my server. WheI had another computer run it I get the following message. However we are using the same versions of gromacs. Back Off! I just backed up md.log to ./#md.log.2# --- Program mdrun, VERSION 4.0.5 Source code file: tpxio.c, line: 1643 Fatal error: Can not read file topol.tpr, this file is from a Gromacs version which is older than 2.0 Make a new one with grompp or use a gro or pdb file, if possible --- I'd say it's evident that if the file is not corrupted (use gmxcheck), the GROMACS installations weren't the same (unmodified) version. Reproduce the conditions and run grompp -h to inspect the version. Perhaps you are having a problem with a shared-library mismatch. If you have such an old version of GROMACS around, either uninstall it and retire the sysadmin, or send the computer to a museum :-) Mark -- gmx-users mailing list gmx-us...@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- gmx-users mailing list gmx-us...@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- Jack http://drugdiscoveryathome.com http://hydrogenathome.org -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] tpr older version message
I preped this ligand using acpypi followed by grompp grompp -f em.mdp -c ligand_GMX.gro -p ligand_GMX.top I tested this .tpr file on my server. WheI had another computer run it I get the following message. However we are using the same versions of gromacs. Back Off! I just backed up md.log to ./#md.log.2# --- Program mdrun, VERSION 4.0.5 Source code file: tpxio.c, line: 1643 Fatal error: Can not read file topol.tpr, this file is from a Gromacs version which is older than 2.0 Make a new one with grompp or use a gro or pdb file, if possible --- -- Jack http://drugdiscoveryathome.com http://hydrogenathome.org -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] Frequency confout is updated
Hello, I would like to setup a screensaver to visualize structures as we are simulating them. We want to avoid slowing down the simulation significantly. I found a solution that read pdb files. Is there a way to reduce the frequency mdrun updates the confout.gro? The structure file (-c) contains the coordinates and velocities of the last step -c confout.gro Output Structure file: gro g96 pdb if I increase these values, does it write to these files less frequently or are we stuck with the updating this structure every step? nstxout: (100) [steps] frequency to write coordinates to output trajectory file, the last coordinates are always written nstvout: (100) [steps] frequency to write velocities to output trajectory, the last velocities are always written -- Jack http://drugdiscoveryathome.com http://hydrogenathome.org -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] combining minimization and md
I was wondering, is there a way you can prepare the parameter files so it will do a minimization followed by molecular dynamics? I think its a feature some other Molecular Dynamics apps support but I have not seen any example mdp files that describe this. -- Jack http://drugdiscoveryathome.com http://hydrogenathome.org -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] Reducing Standard Error output
Apparently this code is only used if the app is in verbose mode. So I guess we have two choices: 1) either find the cause of the lincs warnings That is always necessary if you don't want an expensive random number generator. Your simulation system is ill conditioned, and the lincs warnings will exist and be reported in at least the .log file regardless of the verbosity. Initialy we had this minimized using these parameters define = -DFLEXIBLE integrator = cg ; steep nsteps = 200 constraints = none emtol = 1000 nstcgsteep = 10 ; do a steep every 10 steps of cg emstep = 0.01 ; used with steep nstcomm = 1 coulombtype = PME ns_type = grid rlist = 1.0 rcoulomb = 1.0 rvdw = 1.4 Tcoupl = no Pcoupl = no gen_vel = no nstxout = 0 ; write coords every # step optimize_fft = yes (I borrowed it from acpypi tutorial) Apparently this does not minimize the system quite enough. So I am now reducing emtol to 10 and nsteps to 10,000. I will see if I get convergence. Are there other recomendations regarding minimization? Should we consider constraining the molecule? One idea is 1st minimization with constraints 2nd minimization without constraints 3rd md with constraints 4th md without constraints -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] Grompp failed under double precision
We have a workflow going, and I switched to double precision because of the LINCS issues. I got this error now with grompp. I don't think anything else is different other than double precision, but I included the logs for this. --- Program grompp_d, VERSION 4.0.5 Source code file: toppush.c, line: 1273 Fatal error: [ file spce.itp, line 32 ]: Atom index (1) in bonds out of bounds (1-0). This probably means that you have inserted topology section bonds in a part belonging to a different molecule than you intended to. In that case move the bonds section to the right molecule. --- -- Jack http://drugdiscoveryathome.com http://hydrogenathome.org Name main::make_ndx used only once: possible typo at bin/mdrun.pl line 45. Name main::rsc_memory_bound used only once: possible typo at bin/mdrun.pl line 23. Name main::g_energy used only once: possible typo at bin/mdrun.pl line 47. Name main::protein_lig used only once: possible typo at bin/mdrun.pl line 46. Name main::TOP_SCORE used only once: possible typo at bin/mdrun.pl line 482. 4 Checking if script is running php clear_assignments.php mkdir /home/boincadm/projects/DrugDiscovery/sample_results/tmp mv /home/boincadm/projects/DrugDiscovery/sample_results/autodock_*.7z /home/boincadm/projects/DrugDiscovery/sample_results/tmp 4 Checking if script is running /home/boincadm/projects/DrugDiscovery/sample_results/tmp/autodock_ga_run_10_bt_fzd8min_renum_SS.pdb_lig_omega_70_ts_1260032146055243000.7z rm -rf /home/boincadm/projects/DrugDiscovery/sample_results/tmp/autodock_ga_run_10_bt_fzd8min_renum_SS.pdb_lig_omega_70_ts_1260032146055243000 mkdir /home/boincadm/projects/DrugDiscovery/sample_results/tmp/autodock_ga_run_10_bt_fzd8min_renum_SS.pdb_lig_omega_70_ts_1260032146055243000 cp /home/boincadm/projects/DrugDiscovery/bin/receptor.pdb /home/boincadm/projects/DrugDiscovery/sample_results/tmp/autodock_ga_run_10_bt_fzd8min_renum_SS.pdb_lig_omega_70_ts_1260032146055243000 7za e -y -o/home/boincadm/projects/DrugDiscovery/sample_results/tmp/autodock_ga_run_10_bt_fzd8min_renum_SS.pdb_lig_omega_70_ts_1260032146055243000 /home/boincadm/projects/DrugDiscovery/sample_results/tmp/autodock_ga_run_10_bt_fzd8min_renum_SS.pdb_lig_omega_70_ts_1260032146055243000.7z 7-Zip (A) 4.61 beta Copyright (c) 1999-2008 Igor Pavlov 2008-11-23 p7zip Version 4.61 (locale=en_US.UTF-8,Utf16=on,HugeFiles=on,2 CPUs) Processing archive: /home/boincadm/projects/DrugDiscovery/sample_results/tmp/autodock_ga_run_10_bt_fzd8min_renum_SS.pdb_lig_omega_70_ts_1260032146055243000.7z Extracting out.dlg Extracting job.xml Extracting ligand_receptor.dpf Extracting out.glg Extracting receptor.gpf Everything is Ok Files: 5 Size: 553641 Compressed: 56651 /usr/local/bin/pythonsh /usr/local/MGLTools-1.5.4/MGLToolsPckgs/AutoDockTools/Utilities24/summarize_results4.py -v -d /home/boincadm/projects/DrugDiscovery/sample_results/tmp/autodock_ga_run_10_bt_fzd8min_renum_SS.pdb_lig_omega_70_ts_1260032146055243000 -r receptor.pdb -o /home/boincadm/projects/DrugDiscovery/sample_results/tmp/autodock_ga_run_10_bt_fzd8min_renum_SS.pdb_lig_omega_70_ts_1260032146055243000_summary.txt setting PYTHONHOME environment set verbose to True set directory to /home/boincadm/projects/DrugDiscovery/sample_results/tmp/autodock_ga_run_10_bt_fzd8min_renum_SS.pdb_lig_omega_70_ts_1260032146055243000 set receptor_filename to receptor.pdb set outputfilename to /home/boincadm/projects/DrugDiscovery/sample_results/tmp/autodock_ga_run_10_bt_fzd8min_renum_SS.pdb_lig_omega_70_ts_1260032146055243000_summary.txt first is True rm -rf /home/boincadm/projects/DrugDiscovery/sample_results/tmp/autodock_ga_run_10_bt_fzd8min_renum_SS.pdb_lig_omega_70_ts_1260032146055243000 5 Checking if script is running /home/boincadm/projects/DrugDiscovery/sample_results/tmp/autodock_ga_run_10_bt_fzd8min_renum_SS.pdb_lig_omega_000248_ts_126004461468646.7z rm -rf /home/boincadm/projects/DrugDiscovery/sample_results/tmp/autodock_ga_run_10_bt_fzd8min_renum_SS.pdb_lig_omega_000248_ts_126004461468646 mkdir /home/boincadm/projects/DrugDiscovery/sample_results/tmp/autodock_ga_run_10_bt_fzd8min_renum_SS.pdb_lig_omega_000248_ts_126004461468646 cp /home/boincadm/projects/DrugDiscovery/bin/receptor.pdb /home/boincadm/projects/DrugDiscovery/sample_results/tmp/autodock_ga_run_10_bt_fzd8min_renum_SS.pdb_lig_omega_000248_ts_126004461468646 7za e -y -o/home/boincadm/projects/DrugDiscovery/sample_results/tmp/autodock_ga_run_10_bt_fzd8min_renum_SS.pdb_lig_omega_000248_ts_126004461468646 /home/boincadm/projects/DrugDiscovery/sample_results/tmp/autodock_ga_run_10_bt_fzd8min_renum_SS.pdb_lig_omega_000248_ts_126004461468646.7z 7-Zip (A) 4.61 beta Copyright (c) 1999-2008 Igor Pavlov 2008-11-23 p7zip Version 4.61 (locale=en_US.UTF-8,Utf16=on,HugeFiles=on,2 CPUs) Processing
Re: [gmx-users] Reducing Standard Error output
Even though I can sucessfully run this when I remove the verbose flag, it causes another problem. We keep trac of the progress of indivual simulations using a code modfication in sim_util.c 124: f = fopen(progress.txt, w); 125- if (!f) return; 126- fprintf(f, %g, (step - ir-init_step) / (float) ir-nsteps); 127- fclose(f); Apparently this code is only used if the app is in verbose mode. So I guess we have two choices: 1) either find the cause of the lincs warnings 2) modify the code so it reports progress regardless of verbose flag On Thu, Dec 3, 2009 at 7:39 PM, Jack Shultz j...@drugdiscoveryathome.com wrote: yes the environment I was running in was the boinc wrapper and its supposed to somehow return the standard error output. It probably got overloaded. It is curious why I only had the problem on windows 64 but I'm not going to worry about it. On Thu, Dec 3, 2009 at 6:33 PM, Mark Abraham mark.abra...@anu.edu.au wrote: Jack Shultz wrote: Thanks, I just figured out removing the -v will reduce output. Interestingly I only have this problem with 64-bit Windows hosts. I have not observed it in any others and I have a fairly diverse environment on this project. For now I can say removing the -v gets the app to finish the run. mdrun -v will have no effect on correct completion, unless the use of -v is causing some I/O buffer external to GROMACS to over-run. I suspect your observation indicates you were comparing apples and oranges. Mark -- gmx-users mailing list gmx-us...@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- Jack http://drugdiscoveryathome.com http://hydrogenathome.org -- Jack http://drugdiscoveryathome.com http://hydrogenathome.org -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] Reducing Standard Error output
Our first run typically produces this output Getting Loaded... Reading file md.tpr, VERSION 4.0.5 (single precision) Loaded with Money starting mdrun 'Protein in water' 500 steps, 1.0 ps. step 0 step 100, remaining runtime:95 s Fraction complete: 0.2 step 200, remaining runtime:70 s Fraction complete: 0.4 step 300, remaining runtime:46 s Fraction complete: 0.6 step 400, remaining runtime:23 s Fraction complete: 0.8 Writing final coordinates. step 500, remaining runtime: 0 s Fraction complete: 1 Parallel run - timing based on wallclock. NODE (s) Real (s) (%) Time:119.000119.000100.0 1:59 (Mnbf/s) (GFlops) (ns/day) (hour/ns) Performance: 55.372 3.138 0.728 32.990 gcq#0: Thanx for Using GROMACS - Have a Nice Day For our project's workflow we are extending the simulations using these arguments, -v -x -c -o -e -cpo next.cpt -cpi md.cpt -deffnm md but I notice there is much more standard error output than I was expecting, in addition to a LINCS WARNING. Should I be worried about that warning? Is there a way we can turn off these error reports for each timestep? Step 785, time 1.57 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.051275, max 3.234419 (between atoms 2396 and 2397) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 2396 2397 103.70.0973 0.4065 0.0960 Step 786, time 1.572 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.31, max 0.001926 (between atoms 2396 and 2397) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 2396 2397 69.50.4065 0.0962 0.0960 -- Jack http://drugdiscoveryathome.com http://hydrogenathome.org -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] Reducing Standard Error output
Thanks, I just figured out removing the -v will reduce output. Interestingly I only have this problem with 64-bit Windows hosts. I have not observed it in any others and I have a fairly diverse environment on this project. For now I can say removing the -v gets the app to finish the run. Jack On Thu, Dec 3, 2009 at 10:36 AM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Jack, The option -v is for verbose output. The LINCS warnings may indicate an issue regarding the stability of your system. They usually precede crashes. Maybe you need to equilibrate a bit further. Hope it helps, Tsjerk On Thu, Dec 3, 2009 at 1:26 PM, Jack Shultz j...@drugdiscoveryathome.com wrote: Our first run typically produces this output Getting Loaded... Reading file md.tpr, VERSION 4.0.5 (single precision) Loaded with Money starting mdrun 'Protein in water' 500 steps, 1.0 ps. step 0 step 100, remaining runtime: 95 s Fraction complete: 0.2 step 200, remaining runtime: 70 s Fraction complete: 0.4 step 300, remaining runtime: 46 s Fraction complete: 0.6 step 400, remaining runtime: 23 s Fraction complete: 0.8 Writing final coordinates. step 500, remaining runtime: 0 s Fraction complete: 1 Parallel run - timing based on wallclock. NODE (s) Real (s) (%) Time: 119.000 119.000 100.0 1:59 (Mnbf/s) (GFlops) (ns/day) (hour/ns) Performance: 55.372 3.138 0.728 32.990 gcq#0: Thanx for Using GROMACS - Have a Nice Day For our project's workflow we are extending the simulations using these arguments, -v -x -c -o -e -cpo next.cpt -cpi md.cpt -deffnm md but I notice there is much more standard error output than I was expecting, in addition to a LINCS WARNING. Should I be worried about that warning? Is there a way we can turn off these error reports for each timestep? Step 785, time 1.57 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.051275, max 3.234419 (between atoms 2396 and 2397) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 2396 2397 103.7 0.0973 0.4065 0.0960 Step 786, time 1.572 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.31, max 0.001926 (between atoms 2396 and 2397) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 2396 2397 69.5 0.4065 0.0962 0.0960 -- Jack http://drugdiscoveryathome.com http://hydrogenathome.org -- gmx-users mailing list gmx-us...@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- Tsjerk A. Wassenaar, Ph.D. Computational Chemist Medicinal Chemist Neuropharmacologist -- gmx-users mailing list gmx-us...@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- Jack http://drugdiscoveryathome.com http://hydrogenathome.org -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] Reducing Standard Error output
yes the environment I was running in was the boinc wrapper and its supposed to somehow return the standard error output. It probably got overloaded. It is curious why I only had the problem on windows 64 but I'm not going to worry about it. On Thu, Dec 3, 2009 at 6:33 PM, Mark Abraham mark.abra...@anu.edu.au wrote: Jack Shultz wrote: Thanks, I just figured out removing the -v will reduce output. Interestingly I only have this problem with 64-bit Windows hosts. I have not observed it in any others and I have a fairly diverse environment on this project. For now I can say removing the -v gets the app to finish the run. mdrun -v will have no effect on correct completion, unless the use of -v is causing some I/O buffer external to GROMACS to over-run. I suspect your observation indicates you were comparing apples and oranges. Mark -- gmx-users mailing list gmx-us...@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- Jack http://drugdiscoveryathome.com http://hydrogenathome.org -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] Gromacs with QMMM Support
Thanks. I see MOPAC7 is in the public domain. That way I can use it on my project! 1 The original copyright notice of MOPAC7: 2 3 C 4 C Notice of Public Domain nature of MOPAC 5 C 6 C 'This computer program is a work of the United States 7 C Government and as such is not subject to protection by 8 C copyright (17 U.S.C. # 105.) Any person who fraudulently 9 C places a copyright notice or does any other act contrary 10 C to the provisions of 17 U.S. Code 506(c) shall be subject 11 C to the penalties provided therein. This notice shall not 12 C be altered or removed from this software and is to be on 13 C all reproductions.' 14 C 15 16 Changes made to MOPAC7 code in this work may be used/distributed under the 17 same rules as the original MOPAC7 package; this work is in Public Domain. On Mon, Nov 30, 2009 at 2:50 AM, ilona.bal...@bioquant.uni-heidelberg.de wrote: yes, that's right ;) Quoting Jack Shultz j...@drugdiscoveryathome.com: I am reading this page http://wwwuser.gwdg.de/~ggroenh/qmmm.html Is it correct to assume you need one of the following to compile Gromacs with QMMM support? Gaussian GAMESS-UK MOPAC7 or mopac7.tar.gz -- Jack http://drugdiscoveryathome.com http://hydrogenathome.org -- gmx-users mailing list gmx-us...@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- gmx-users mailing list gmx-us...@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use thewww interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Jack http://drugdiscoveryathome.com http://hydrogenathome.org -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] Gromacs with QMMM Support
I am reading this page http://wwwuser.gwdg.de/~ggroenh/qmmm.html Is it correct to assume you need one of the following to compile Gromacs with QMMM support? Gaussian GAMESS-UK MOPAC7 or mopac7.tar.gz -- Jack http://drugdiscoveryathome.com http://hydrogenathome.org -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] Continue simulation
Is it ok just to use tpbconv, even though we get this message Continuation should be done by loading a checkpoint file with mdrun -cpi? ++ I have tried mdrun using the -cpi flag mdrun -v -x -c -o -e -cpo next.cpt -cpi md.cpt -deffnm md Then when I run the next using the next.cpt, it seems to do the next time interval because it is actually taking time to compute timesteps mdrun -v -x -c -o -e -cpo next2.cpt -cpi next.cpt -deffnm md using the checkpoint, i get less standard output telling me the tototal simulation time while preping the mdrun using tpbconv -s md.tpr -f md.trr -e md.edr -time 2 -o next.tpr I get this output. starting mdrun 'Protein in water' 1500 steps, 3.0 ps (continuing from step 500, 1.0 ps). step 500, will finish Wed Nov 25 00:15:43 2009 step 700, remaining runtime: 258 s So should there be any difference in the results then? -- Jack http://drugdiscoveryathome.com http://hydrogenathome.org -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] User results for another run
I must have asked this before but I'm trying find the answer again. If I want to use the results from mdrun for another run following the first time interval, what do I need to do? -- Jack http://drugdiscoveryathome.com http://hydrogenathome.org -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] Invoking parameters at startup
I am trying to specify protein and LIG as groups when I start certain analysis programs. I want to run this as part of a script. For example, if I want to run g_rms it will prompt me to specify the two groups we want to compare. I want to specify the groups when I start the app. Other than re-writing the command arguments in the app, is there a way to pass those parameters at startup? -- Jack http://drugdiscoveryathome.com http://hydrogenathome.org -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] Invoking parameters at startup
Ah yes thanks I came up with it after a little more testing. c:\ProgramData\BOINC\slots\4echo LIG protein | g_rms.exe -s md.tpr -f md.xtc -n index.ndx -nice 19 On Fri, Nov 13, 2009 at 6:56 PM, Justin A. Lemkul jalem...@vt.edu wrote: Jack Shultz wrote: I am trying to specify protein and LIG as groups when I start certain analysis programs. I want to run this as part of a script. For example, if I want to run g_rms it will prompt me to specify the two groups we want to compare. I want to specify the groups when I start the app. Other than re-writing the command arguments in the app, is there a way to pass those parameters at startup? Something like this? http://www.gromacs.org/Documentation/How-tos/Making_Commands_Non-Interactive -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing list gmx-us...@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- Jack http://drugdiscoveryathome.com http://hydrogenathome.org -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] Generate an Index File
I am trying to run g_dist c:\ProgramData\BOINC\slots\0g_dist.exe -f md.xtc -s md.tpr --- Program g_dist, VERSION 4.0.5 Source code file: futil.c, line: 330 File input/output error: index.ndx --- Thanx for Using GROMACS - Have a Nice Day so I tried mdrun with the -dn option mdrun.exe -dn -v -x -deffnm md It failed to generate an index file. What am I doing wrong? -- Jack http://drugdiscoveryathome.com http://hydrogenathome.org -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] Re: Remove solvent from results
I guess it can be done with sed but is there another way using one of the Gromacs apps? On Tue, Nov 10, 2009 at 12:48 PM, Jack Shultz j...@drugdiscoveryathome.com wrote: Hi Guys, I was wondering if there is any way to remove the solvent from your final trajectory results in mdrun? -- Jack http://drugdiscoveryathome.com http://hydrogenathome.org -- Jack http://drugdiscoveryathome.com http://hydrogenathome.org -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] Remove solvent from results
Hi Guys, I was wondering if there is any way to remove the solvent from your final trajectory results in mdrun? -- Jack http://drugdiscoveryathome.com http://hydrogenathome.org -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] How to generate xvg files
Hi I am trying to generate xvg files for my simulation. Which parameter do I need to specify? -- Jack http://drugdiscoveryathome.com http://hydrogenathome.org -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] How to generate xvg files
Actually I guess I need to generate the xtc first before I can get the xvg I am trying to develop a workflow for this mdrun g dist calculates the distances between the centers of mass of two groups g bond calculates distances between atoms g msd calculates mean square displacements g rms calculates rmsd’s with a reference structure and rmsd matrices g rmsf calculates atomic fluctuations g energy writes energies to xvg files and displays averages On Tue, Nov 10, 2009 at 9:24 PM, Amit Choubey kgp.a...@gmail.com wrote: On Tue, Nov 10, 2009 at 6:11 PM, Jack Shultz j...@drugdiscoveryathome.com wrote: Hi I am trying to generate xvg files for my simulation. Which parameter do I need to specify? xvg files for what? They are used for data files for 2D plots of quantities that can be analyzed... Can you be more specific? amit -- Jack http://drugdiscoveryathome.com http://hydrogenathome.org -- gmx-users mailing list gmx-us...@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- gmx-users mailing list gmx-us...@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- Jack http://drugdiscoveryathome.com http://hydrogenathome.org -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] How to generate xvg files
I'm trying to get the xtc output. The mdp file has these parameters. Is the nstxtcout what specifiies it to generate xtc? nsteps = 2000 ; Maximum number of (minimization) steps to perform nstenergy = 10; Write energies to disk every nstenergy steps nstxtcout = 10; Write coordinates to disk every nstxtcout steps Do I need to use this -x flag? mdrun -nice 0 -s em.tpr -x No xtc was created though On Tue, Nov 10, 2009 at 9:43 PM, Amit Choubey kgp.a...@gmail.com wrote: On Tue, Nov 10, 2009 at 6:31 PM, Jack Shultz j...@drugdiscoveryathome.com wrote: Actually I guess I need to generate the xtc first before I can get the xvg I am trying to develop a workflow for this mdrun g dist calculates the distances between the centers of mass of two groups g bond calculates distances between atoms g msd calculates mean square displacements g rms calculates rmsd’s with a reference structure and rmsd matrices g rmsf calculates atomic fluctuations g energy writes energies to xvg files and displays averages Thats true. First you need to do the simulation 'mdrun' and then analyze the trajectory (.xtc) and energy (.edr) files generated. It takes quite some time to figure out the first step 'mdrun' :) amit On Tue, Nov 10, 2009 at 9:24 PM, Amit Choubey kgp.a...@gmail.com wrote: On Tue, Nov 10, 2009 at 6:11 PM, Jack Shultz j...@drugdiscoveryathome.com wrote: Hi I am trying to generate xvg files for my simulation. Which parameter do I need to specify? xvg files for what? They are used for data files for 2D plots of quantities that can be analyzed... Can you be more specific? amit -- Jack http://drugdiscoveryathome.com http://hydrogenathome.org -- gmx-users mailing list gmx-us...@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- gmx-users mailing list gmx-us...@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- Jack http://drugdiscoveryathome.com http://hydrogenathome.org -- gmx-users mailing list gmx-us...@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- gmx-users mailing list gmx-us...@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- Jack http://drugdiscoveryathome.com http://hydrogenathome.org -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] Missing H from residue
I tried to protonate my pdb file using openbabel babel -ipdb fzd8min_renum_SS.pdb -opdb Protein.pdb -h Then I ran pdb2gmx with the following pdb2gmx -ff amber99sb -f ProteinAmber.pdb -o Protein2.pdb -p Protein.top -water spce -ignh But apparently I am missing a H from my first residue. Is there an easy way to add missing atoms? WARNING: atom H is missing in residue GLU 1 in the pdb file You might need to add atom H to the hydrogen database of residue GLU in the file ff???.hdb (see the manual) --- Program pdb2gmx, VERSION 4.0.5 Source code file: pdb2top.c, line: 704 Fatal error: There were 1 missing atoms in molecule Protein, if you want to use this incomplete topology anyhow, use the option -missing --- -- Jack http://drugdiscoveryathome.com http://hydrogenathome.org -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] Missing H from residue
Well I was just wondering if there was some porgram that could add this atom automatically. It looks like this H is missing. I supposed I could re-write the pdb file. It has all these non-standard Hydrogens. HB, HG and HT. Maybe I can just replace those. This is the residue in question ATOM 1 N GLU32 -20.050 8.920 -4.700 1.00 0.00 N ATOM 2 CA GLU32 -19.847 8.507 -3.304 1.00 0.00 C ATOM 3 C GLU32 -20.807 7.451 -2.751 1.00 0.00 C ATOM 4 O GLU32 -21.843 7.183 -3.340 1.00 0.00 O ATOM 5 CB GLU32 -19.913 9.782 -2.416 1.00 0.00 C ATOM 6 CG GLU32 -18.641 10.678 -2.498 1.00 0.00 C ATOM 7 CD GLU32 -18.573 11.627 -1.334 1.00 0.00 C ATOM 8 OE1 GLU32 -19.009 12.797 -1.488 1.00 0.00 O ATOM 9 OE2 GLU32 -18.089 11.174 -0.257 1.00 0.00 O ATOM 10 HA GLU32 -18.845 8.057 -3.227 1.00 0.00 H ATOM 11 HB1 GLU32 -20.805 10.368 -2.695 1.00 0.00 H ATOM 12 HB2 GLU32 -20.026 9.493 -1.358 1.00 0.00 H ATOM 13 HG1 GLU32 -17.724 10.072 -2.453 1.00 0.00 H ATOM 14 HG2 GLU32 -18.628 11.255 -3.435 1.00 0.00 H ATOM 15 HT2 GLU32 -19.381 9.526 -5.140 1.00 0.00 H ATOM 16 HT1 GLU32 -20.892 8.644 -5.172 1.00 0.00 H [boinc...@vps test]$ grep -A5 GLU /usr/local/gromacs/share/gromacs/top/ffamber99sb.* /usr/local/gromacs/share/gromacs/top/ffamber99sb.hdb:GLU4 /usr/local/gromacs/share/gromacs/top/ffamber99sb.hdb-1 1 H N -C CA /usr/local/gromacs/share/gromacs/top/ffamber99sb.hdb-1 5 HA CA N CB C /usr/local/gromacs/share/gromacs/top/ffamber99sb.hdb-2 6 HB CB CA CG /usr/local/gromacs/share/gromacs/top/ffamber99sb.hdb-2 6 HG CG CB CD /usr/local/gromacs/share/gromacs/top/ffamber99sb.hdb-ASP3 /usr/local/gromacs/share/gromacs/top/ffamber99sb.rtp.bad:[ GLU ] /usr/local/gromacs/share/gromacs/top/ffamber99sb.rtp.bad- [ atoms ] /usr/local/gromacs/share/gromacs/top/ffamber99sb.rtp.bad- N amber99sb_34 -0.51630 1 /usr/local/gromacs/share/gromacs/top/ffamber99sb.rtp.bad- H amber99sb_17 0.29360 2 /usr/local/gromacs/share/gromacs/top/ffamber99sb.rtp.bad-CA amber99sb_11 0.03970 3 /usr/local/gromacs/share/gromacs/top/ffamber99sb.rtp.bad-HA amber99sb_19 0.11050 4 On Mon, Nov 9, 2009 at 4:26 PM, Mark Abraham mark.abra...@anu.edu.au wrote: Jack Shultz wrote: I tried to protonate my pdb file using openbabel babel -ipdb fzd8min_renum_SS.pdb -opdb Protein.pdb -h Then I ran pdb2gmx with the following pdb2gmx -ff amber99sb -f ProteinAmber.pdb -o Protein2.pdb -p Protein.top -water spce -ignh But apparently I am missing a H from my first residue. Is there an easy way to add missing atoms? Yep - you may need a well-formatted .hdb file, like the message says :-) You should check out whether the AMBER port you installed supports this feature or not. Alternatively, have a look in the file and with a viewer to see what is present for residue 1 and how the atoms are named, and whether renaming some atoms will fix the issue. Mark WARNING: atom H is missing in residue GLU 1 in the pdb file You might need to add atom H to the hydrogen database of residue GLU in the file ff???.hdb (see the manual) --- Program pdb2gmx, VERSION 4.0.5 Source code file: pdb2top.c, line: 704 Fatal error: There were 1 missing atoms in molecule Protein, if you want to use this incomplete topology anyhow, use the option -missing --- -- gmx-users mailing list gmx-us...@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- Jack http://drugdiscoveryathome.com http://hydrogenathome.org -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] Missing H from residue
I modified the N-Terminal and C-Terminal Residues. [boinc...@vps test]$ grep NGLU ProteinAmber.pdb grep CARG ProteinAmber.pdb ATOM 1 N NGLU 32 -20.050 8.920 -4.700 1.00 0.00 N ATOM 2 CA NGLU 32 -19.847 8.507 -3.304 1.00 0.00 C ATOM 3 C NGLU 32 -20.807 7.451 -2.751 1.00 0.00 C ATOM 4 O NGLU 32 -21.843 7.183 -3.340 1.00 0.00 O ATOM 5 CB NGLU 32 -19.913 9.782 -2.416 1.00 0.00 C ATOM 6 CG NGLU 32 -18.641 10.678 -2.498 1.00 0.00 C ATOM 7 CD NGLU 32 -18.573 11.627 -1.334 1.00 0.00 C ATOM 8 OE1 NGLU 32 -19.009 12.797 -1.488 1.00 0.00 O ATOM 9 OE2 NGLU 32 -18.089 11.174 -0.257 1.00 0.00 O ATOM 10 HA NGLU 32 -18.845 8.057 -3.227 1.00 0.00 H ATOM 11 HB1 NGLU 32 -20.805 10.368 -2.695 1.00 0.00 H ATOM 12 HB2 NGLU 32 -20.026 9.493 -1.358 1.00 0.00 H ATOM 13 HG1 NGLU 32 -17.724 10.072 -2.453 1.00 0.00 H ATOM 14 HG2 NGLU 32 -18.628 11.255 -3.435 1.00 0.00 H ATOM 15 HT2 NGLU 32 -19.381 9.526 -5.140 1.00 0.00 H ATOM 16 HT1 NGLU 32 -20.892 8.644 -5.172 1.00 0.00 H ATOM 3819 N CARG 153 -2.889 -18.736 0.849 1.00 0.00 N ATOM 3820 CA CARG 153 -4.210 -19.301 1.173 1.00 0.00 C ATOM 3821 C CARG 153 -4.155 -20.743 1.653 1.00 0.00 C ATOM 3822 O CARG 153 -4.455 -21.080 2.791 1.00 0.00 O ATOM 3823 CB CARG 153 -5.123 -19.172 -0.074 1.00 0.00 C ATOM 3824 CG CARG 153 -5.347 -17.677 -0.414 1.00 0.00 C ATOM 3825 CD CARG 153 -6.074 -17.485 -1.764 1.00 0.00 C ATOM 3826 NE CARG 153 -7.488 -17.868 -1.625 1.00 0.00 N ATOM 3827 CZ CARG 153 -8.038 -19.003 -1.986 1.00 0.00 C ATOM 3828 NH1 CARG 153 -7.368 -20.017 -2.446 1.00 0.00 N ATOM 3829 NH2 CARG 153 -9.327 -19.146 -1.882 1.00 0.00 N ATOM 3830 HA CARG 153 -4.670 -18.715 1.987 1.00 0.00 H ATOM 3831 OXT CARG 153 -3.778 -21.646 0.751 1.00 0.00 O ATOM 3832 HT CARG 153 -3.770 -22.506 1.154 1.00 0.00 H ATOM 3833 HB1 CARG 153 -4.628 -19.690 -0.911 1.00 0.00 H ATOM 3834 HB2 CARG 153 -6.096 -19.657 0.114 1.00 0.00 H ATOM 3835 HG1 CARG 153 -5.942 -17.224 0.393 1.00 0.00 H ATOM 3836 HG2 CARG 153 -4.393 -17.125 -0.460 1.00 0.00 H ATOM 3837 HD1 CARG 153 -6.049 -16.397 -1.960 1.00 0.00 H ATOM 3838 HD2 CARG 153 -5.519 -17.914 -2.612 1.00 0.00 H ATOM 3839 HE CARG 153 -8.133 -17.122 -1.290 1.00 0.00 H ATOM 3840 1HH1 CARG 153 -7.834 -20.881 -2.736 1.00 0.00 H ATOM 3841 2HH1 CARG 153 -6.359 -19.962 -2.559 1.00 0.00 H ATOM 3842 1HH2 CARG 153 -9.802 -20.000 -2.173 1.00 0.00 H ATOM 3843 2HH2 CARG 153 -9.904 -18.331 -1.627 1.00 0.00 H ATOM 3844 HN CARG 153 -2.612 -18.555 -0.097 1.00 0.00 H TER3845 CARG 153 This time I did not protonate with babel pdb2gmx -ff amber99sb -f ProteinAmber.pdb -ignh Back Off! I just backed up topol.top to ./#topol.top.6# Processing chain 1 (1976 atoms, 244 residues) There are 362 donors and 364 acceptors There are 561 hydrogen bonds --- Program pdb2gmx, VERSION 4.0.5 Source code file: pdb2gmx.c, line: 429 Fatal error: Atom O in residue CARG 244 not found in rtp entry with 25 atoms while sorting atoms --- But we got an O here ATOM 3822 O CARG 153 -4.455 -21.080 2.791 1.00 0.00 O On Mon, Nov 9, 2009 at 6:54 PM, Mark Abraham mark.abra...@anu.edu.au wrote: Jack Shultz wrote: Well I was just wondering if there was some porgram that could add this atom automatically. It looks like this H is missing. I supposed I could re-write the pdb file. It has all these non-standard Hydrogens. HB, HG and HT. Maybe I can just replace those. Non-standard? H[ABGDEZ][123] are the H atoms for the heavy atom that is alpha through zeta to the backbone carbonyl. This is the residue in question ATOM 1 N GLU 32 -20.050 8.920 -4.700 1.00 0.00 N ATOM 2 CA GLU 32 -19.847 8.507 -3.304 1.00 0.00 C ATOM 3 C GLU 32 -20.807 7.451 -2.751 1.00 0.00 C ATOM 4 O GLU 32 -21.843 7.183 -3.340 1.00 0.00 O ATOM 5 CB GLU 32 -19.913 9.782 -2.416 1.00 0.00 C ATOM 6 CG GLU 32 -18.641 10.678 -2.498 1.00 0.00 C ATOM 7 CD GLU 32 -18.573 11.627 -1.334 1.00 0.00 C ATOM
Re: [gmx-users] Missing H from residue
On Mon, Nov 9, 2009 at 8:35 PM, Justin A. Lemkul jalem...@vt.edu wrote: Jack Shultz wrote: snip --- Program pdb2gmx, VERSION 4.0.5 Source code file: pdb2gmx.c, line: 429 Fatal error: Atom O in residue CARG 244 not found in rtp entry with 25 atoms while sorting atoms --- But we got an O here ATOM 3822 O CARG 153 -4.455 -21.080 2.791 1.00 0.00 O The error is not telling you that the O atom is missing from the .pdb file; it is telling you that it is present in the .pdb, but not in the .rtp entry. Look at the .rtp entry for CARG [ CARG ] [ atoms ] Namber99_34 -0.34810 1 Hamber99_17 0.27640 2 CAamber99_11 -0.30680 3 HAamber99_19 0.14470 4 CBamber99_11 -0.03740 5 HB1amber99_18 0.03710 6 HB2amber99_18 0.03710 7 CGamber99_11 0.07440 8 HG1amber99_18 0.01850 9 HG2amber99_18 0.0185010 CDamber99_11 0.1114011 HD1amber99_19 0.0468012 HD2amber99_19 0.0468013 NEamber99_38 -0.5564014 HEamber99_17 0.3479015 CZamber99_30.8368016 NH1amber99_38 -0.8737017 HH11amber99_17 0.4493018 HH12amber99_17 0.4493019 NH2amber99_38 -0.8737020 HH21amber99_17 0.4493021 HH22amber99_17 0.4493022 Camber99_20.8557023 OC1amber99_45 -0.8266024 OC2amber99_45 -0.8266025 - you should have an O1 and O2 atom for the I made the following modification ATOM 1900 O1 CARG 153 -17.391 -20.267 11.508 1.00 0.00 O ATOM 1909 O2 CARG 153 -18.666 -19.390 13.107 1.00 0.00 O --- Program pdb2gmx, VERSION 4.0.5 Source code file: pdb2gmx.c, line: 429 Fatal error: Atom O in residue CARG 122 not found in rtp entry with 25 atoms while sorting atoms --- C-terminal carboxylate. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing list gmx-us...@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- Jack http://drugdiscoveryathome.com http://hydrogenathome.org -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] Missing H from residue
Thanks Justin! Got it now. On Mon, Nov 9, 2009 at 10:00 PM, Justin A. Lemkul jalem...@vt.edu wrote: Jack Shultz wrote: On Mon, Nov 9, 2009 at 8:35 PM, Justin A. Lemkul jalem...@vt.edu wrote: Jack Shultz wrote: snip --- Program pdb2gmx, VERSION 4.0.5 Source code file: pdb2gmx.c, line: 429 Fatal error: Atom O in residue CARG 244 not found in rtp entry with 25 atoms while sorting atoms --- But we got an O here ATOM 3822 O CARG 153 -4.455 -21.080 2.791 1.00 0.00 O The error is not telling you that the O atom is missing from the .pdb file; it is telling you that it is present in the .pdb, but not in the .rtp entry. Look at the .rtp entry for CARG [ CARG ] [ atoms ] N amber99_34 -0.34810 1 H amber99_17 0.27640 2 CA amber99_11 -0.30680 3 HA amber99_19 0.14470 4 CB amber99_11 -0.03740 5 HB1 amber99_18 0.03710 6 HB2 amber99_18 0.03710 7 CG amber99_11 0.07440 8 HG1 amber99_18 0.01850 9 HG2 amber99_18 0.01850 10 CD amber99_11 0.11140 11 HD1 amber99_19 0.04680 12 HD2 amber99_19 0.04680 13 NE amber99_38 -0.55640 14 HE amber99_17 0.34790 15 CZ amber99_3 0.83680 16 NH1 amber99_38 -0.87370 17 HH11 amber99_17 0.44930 18 HH12 amber99_17 0.44930 19 NH2 amber99_38 -0.87370 20 HH21 amber99_17 0.44930 21 HH22 amber99_17 0.44930 22 C amber99_2 0.85570 23 OC1 amber99_45 -0.82660 24 OC2 amber99_45 -0.82660 25 - you should have an O1 and O2 atom for the I made the following modification ATOM 1900 O1 CARG 153 -17.391 -20.267 11.508 1.00 0.00 O ATOM 1909 O2 CARG 153 -18.666 -19.390 13.107 1.00 0.00 O Forgive my typo, what I meant was OC1 and OC2. You must always make sure the atoms in the structure file match those expected by the .rtp file. You need OC1 and OC2. -Justin --- Program pdb2gmx, VERSION 4.0.5 Source code file: pdb2gmx.c, line: 429 Fatal error: Atom O in residue CARG 122 not found in rtp entry with 25 atoms while sorting atoms --- C-terminal carboxylate. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing list gmx-us...@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing list gmx-us...@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- Jack http://drugdiscoveryathome.com http://hydrogenathome.org -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] Check out my photos on Facebook
Hi gmx-users@gromacs.org, I set up a Facebook profile where I can post my pictures, videos and events and I want to add you as a friend so you can see it. First, you need to join Facebook! Once you join, you can also create your own profile. Thanks, Jack To sign up for Facebook, follow the link below: http://www.facebook.com/p.php?i=832713248k=S3G2X4U64T6G6BD1PA4UVQSVS6BAZXVDTTEUr Already have an account? Add this email address to your account http://www.facebook.com/n/?merge_accounts.phpi=832713248k=s3g2x4u64t6g6bd1pa4uvqsvs6bazxvdtteu.gmx-us...@gromacs.org was invited to join Facebook by Jack Shultz. If you do not wish to receive this type of email from Facebook in the future, please click on the link below to unsubscribe. http://www.facebook.com/o.php?k=7c1955u=10132975250mid=145814aG5af318674a92G0G8 Facebook's offices are located at 1601 S. California Ave., Palo Alto, CA 94304. ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] Parameter to for randomizing simulation
Hello, What parameter do I set in the mdp file to make it random every time it runs? -- Jack http://drugdiscoveryathome.com http://hydrogenathome.org ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] Parameter to for randomizing simulation
I thought there was a way to introduce the random number generator via the application I was trying to use this parameter Id_seed=-1 but it failed :-( I suppose I can insert a random number to gen_seed every time I submit. is there a range of numbers for gen_seed? On Tue, Sep 29, 2009 at 1:12 PM, Justin A. Lemkul jalem...@vt.edu wrote: Jack Shultz wrote: Hello, What parameter do I set in the mdp file to make it random every time it runs? Random starting velocities? Use different values of gen_seed. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing list gmx-us...@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- Jack http://drugdiscoveryathome.com http://hydrogenathome.org ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] Static build
Thanks, I switched to a fedora VM and it built properly. On Mon, Sep 28, 2009 at 4:26 AM, Ansgar Esztermann aesz...@gwdg.de wrote: On Sep 27, 2009, at 6:24 , Jack Shultz wrote: I'm trying to find a package that distributes libSM.a In case you have trouble finding the correct package: if you are on an rpm-bases system (e.g. Redhat, CentOS, SuSE), try rpm -qf /usr/bin/libSM.so to find the package providing the shared library. The corresponding static lib should be in a package with a similar name, but with a -dev or -devel suffix. A. -- Ansgar Esztermann DV-Systemadministration Max-Planck-Institut für biophysikalische Chemie, Abteilung 105 ___ gmx-users mailing list gmx-us...@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use thewww interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Jack http://drugdiscoveryathome.com http://hydrogenathome.org ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] Static build
I'm trying to find a package that distributes libSM.a On Sat, Sep 26, 2009 at 10:39 PM, Mark Abraham mark.abra...@anu.edu.au wrote: Jack Shultz wrote: Hello, I am trying to build statically with the small source changes I made yesterday. I'm building on 32 bit linux with single precision. I have libSM [r...@vps gromacs-4.0.5]# ls /usr/lib/libSM* /usr/lib/libSM.so /usr/lib/libSM.so.6 /usr/lib/libSM.so.6.0.0 I get this error message cc -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -funroll-all-loops -std=gnu99 -static -o grompp grompp.o -L/usr/lib ./.libs/libgmxpreprocess.a ../mdlib/.libs/libmd.a /root/gromacs-4.0.5/src/gmxlib/.libs/libgmx.a ../gmxlib/.libs/libgmx.a -lnsl -lfftw3f -lm -lSM -lICE -lX11 /usr/bin/ld: cannot find -lSM collect2: ld returned 1 exit status make[3]: *** [grompp] Error 1 make[3]: Leaving directory `/root/gromacs-4.0.5/src/kernel' make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory `/root/gromacs-4.0.5/src' make[1]: *** [all] Error 2 make[1]: Leaving directory `/root/gromacs-4.0.5/src' make: *** [all-recursive] Error 1 I used this flag ./configure CPPFLAGS=-L/usr/lib --enable-all-static You have libSM, but you have only the libraries suitable for dynamic linking. You need /usr/lib/libSM.a on your library search path for static linking. It's slightly superior to use ./configure LIBS=-L/xxx/yyy, but usually equivalent in practice. Mark ___ gmx-users mailing list gmx-us...@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- Jack http://drugdiscoveryathome.com http://hydrogenathome.org ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] Static build
Hello, I am trying to build statically with the small source changes I made yesterday. I'm building on 32 bit linux with single precision. I have libSM [r...@vps gromacs-4.0.5]# ls /usr/lib/libSM* /usr/lib/libSM.so /usr/lib/libSM.so.6 /usr/lib/libSM.so.6.0.0 I get this error message cc -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -funroll-all-loops -std=gnu99 -static -o grompp grompp.o -L/usr/lib ./.libs/libgmxpreprocess.a ../mdlib/.libs/libmd.a /root/gromacs-4.0.5/src/gmxlib/.libs/libgmx.a ../gmxlib/.libs/libgmx.a -lnsl -lfftw3f -lm -lSM -lICE -lX11 /usr/bin/ld: cannot find -lSM collect2: ld returned 1 exit status make[3]: *** [grompp] Error 1 make[3]: Leaving directory `/root/gromacs-4.0.5/src/kernel' make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory `/root/gromacs-4.0.5/src' make[1]: *** [all] Error 2 make[1]: Leaving directory `/root/gromacs-4.0.5/src' make: *** [all-recursive] Error 1 I used this flag ./configure CPPFLAGS=-L/usr/lib --enable-all-static -- Jack http://drugdiscoveryathome.com http://hydrogenathome.org ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] Consecutive Simulations
If I run a simulation using mdrun and then run mdrun again, does it add another interval of simulation or does it just re-run the last simulation. I'll elaborate so it makes a little more sense, our project has this progress bar that tells users the progress of the simulation. If I run mdrun for 100ps they will think it is stuck in an endless loop. If we run increments of mdrun, we can update the bar at each increment. Can we go straight to mdrun or do we have to prep the next increment with grompp? -- Jack http://drugdiscoveryathome.com http://hydrogenathome.org ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] Consecutive Simulations
Thanks Justin, you are very helpful as always :-) On Thu, Sep 24, 2009 at 6:41 AM, Justin A. Lemkul jalem...@vt.edu wrote: Jack Shultz wrote: If I run a simulation using mdrun and then run mdrun again, does it add another interval of simulation or does it just re-run the last simulation. I'll elaborate so it makes a little more sense, our project has this progress bar that tells users the progress of the simulation. If I run mdrun for 100ps they will think it is stuck in an endless loop. If we run increments of mdrun, we can update the bar at each increment. Can we go straight to mdrun or do we have to prep the next increment with grompp? You have to make use of checkpointing. This page might be useful: http://www.gromacs.org/Documentation/How-tos/Extending_Simulations -Justin -- Jack http://drugdiscoveryathome.com http://hydrogenathome.org ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar 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/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/mailing_lists/users.php -- Jack http://drugdiscoveryathome.com http://hydrogenathome.org ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] timestep fraction complete
I figured out another way to update the progress of my simulation, but I need to report the fraction of completion at the certain intervals of mdrun. Possibly at every time step or if that does not make sense every 100 timesteps. I don't think this is a feature currently supported, so I will have to make some source code chages. I am looking for the variables related to total number of time steps and where it controls the the current time step so I can calculate the fraction of complete where current-timestep / total-timestep -- Jack http://drugdiscoveryathome.com http://hydrogenathome.org ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] timestep fraction complete
I am hoping for an update every 10 minutes just to satisfy the anxieties of
volunteers crunching on my project, but every hour may be satisfactory. And
if I can do this without requiring any shell scripts it would be better in
my environment. So I started making some code modifications which apparently
did not work
src/mdlib/sim_util.c:93:void print_time(FILE *out,time_t start,int
step,t_inputrec *ir)
src/mdlib/sim_util.c-94-{
src/mdlib/sim_util.c-95- static real time_per_step;
src/mdlib/sim_util.c-96- static time_t end;
src/mdlib/sim_util.c-97- time_t finish;
src/mdlib/sim_util.c-98- double dt, fc;
src/mdlib/sim_util.c-99- char buf[48];
src/mdlib/sim_util.c-100- FILE *progress=progress.txt;
src/mdlib/sim_util.c-101-
src/mdlib/sim_util.c-102- if (!gmx_parallel_env)
src/mdlib/sim_util.c-103-fprintf(out,\r);
src/mdlib/sim_util.c-104- fprintf(out,step %d,step);
src/mdlib/sim_util.c-105- if ((step = ir-nstlist)) {
src/mdlib/sim_util.c-106-if ((ir-nstlist == 0) || ((step % ir-nstlist)
== 0)) {
src/mdlib/sim_util.c-107- /* We have done a full cycle let's update
time_per_step */
src/mdlib/sim_util.c-108- end=time(NULL);
src/mdlib/sim_util.c-109- dt=difftime(end,start);
src/mdlib/sim_util.c-110- time_per_step=dt/(step - ir-init_step + 1);
src/mdlib/sim_util.c-111-}
src/mdlib/sim_util.c-112-dt=(ir-nsteps + ir-init_step -
step)*time_per_step;
src/mdlib/sim_util.c-113-
src/mdlib/sim_util.c-114-if (dt = 300) {
src/mdlib/sim_util.c-115- finish = end+(time_t)dt;
src/mdlib/sim_util.c-116- sprintf(buf,%s,ctime(finish));
src/mdlib/sim_util.c-117- buf[strlen(buf)-1]='\0';
src/mdlib/sim_util.c-118- fprintf(out,, will finish %s,buf);
src/mdlib/sim_util.c-119-}
src/mdlib/sim_util.c-120-else
src/mdlib/sim_util.c-121- fprintf(out,, remaining runtime: %5d
s ,(int)dt);
src/mdlib/sim_util.c-122- fc = (int)dt / ir-nstlist;
src/mdlib/sim_util.c-123- fprintf(stderr, Fraction complete: %d \n,
fc);
src/mdlib/sim_util.c-124- }
src/mdlib/sim_util.c-125- if (gmx_parallel_env)
src/mdlib/sim_util.c-126-fprintf(out,\n);
src/mdlib/sim_util.c-127-
src/mdlib/sim_util.c-128- fflush(out);
src/mdlib/sim_util.c-129-}
Back Off! I just backed up md.edr to ./#md.edr.4#
starting mdrun 'Protein in water'
500 steps, 1.0 ps.
step 100, remaining runtime: 122 s Fraction complete: 0
step 200, remaining runtime:92 s Fraction complete: 0
On Thu, Sep 24, 2009 at 6:34 PM, Mark Abraham mark.abra...@anu.edu.auwrote:
Jack Shultz wrote:
I figured out another way to update the progress of my simulation, but I
need to report the fraction of completion at the certain intervals of mdrun.
Possibly at every time step or if that does not make sense every 100
timesteps. I don't think this is a feature currently supported, so I will
have to make some source code chages. I am looking for the variables related
to total number of time steps and where it controls the the current time
step so I can calculate the fraction of complete where current-timestep /
total-timestep
Under at least some circumstances GROMACS writes the expected runtime
remaining to stderr, but I don't recall what/when. Piping that to some
useful script has to be a good start. You certainly don't need this data
every time step, and don't want to be perturbing mdrun to get it.
Even if the above was unsuitable, surely progress would only need to be
moderately accurate and for simulations that last many hours. If so, you'll
get good enough data by grepping a gmxdump of the .tpr to get the expected
frequencies of output and length of run, and then watching the growth of
whichever of .log/.trr/.edr is written most frequently. I/O buffering will
affect the numbers somewhat.
Mark
___
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--
Jack
http://drugdiscoveryathome.com
http://hydrogenathome.org
___
gmx-users mailing listgmx-users@gromacs.org
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Re: [gmx-users] timestep fraction complete
Ah of course!
fc = (int)dt / ir-nstlist;
I should cast these as data types that support decimals right?
On Thu, Sep 24, 2009 at 6:44 PM, Jack Shultz
j...@drugdiscoveryathome.comwrote:
I am hoping for an update every 10 minutes just to satisfy the anxieties of
volunteers crunching on my project, but every hour may be satisfactory. And
if I can do this without requiring any shell scripts it would be better in
my environment. So I started making some code modifications which apparently
did not work
src/mdlib/sim_util.c:93:void print_time(FILE *out,time_t start,int
step,t_inputrec *ir)
src/mdlib/sim_util.c-94-{
src/mdlib/sim_util.c-95- static real time_per_step;
src/mdlib/sim_util.c-96- static time_t end;
src/mdlib/sim_util.c-97- time_t finish;
src/mdlib/sim_util.c-98- double dt, fc;
src/mdlib/sim_util.c-99- char buf[48];
src/mdlib/sim_util.c-100- FILE *progress=progress.txt;
src/mdlib/sim_util.c-101-
src/mdlib/sim_util.c-102- if (!gmx_parallel_env)
src/mdlib/sim_util.c-103-fprintf(out,\r);
src/mdlib/sim_util.c-104- fprintf(out,step %d,step);
src/mdlib/sim_util.c-105- if ((step = ir-nstlist)) {
src/mdlib/sim_util.c-106-if ((ir-nstlist == 0) || ((step %
ir-nstlist) == 0)) {
src/mdlib/sim_util.c-107- /* We have done a full cycle let's update
time_per_step */
src/mdlib/sim_util.c-108- end=time(NULL);
src/mdlib/sim_util.c-109- dt=difftime(end,start);
src/mdlib/sim_util.c-110- time_per_step=dt/(step - ir-init_step + 1);
src/mdlib/sim_util.c-111-}
src/mdlib/sim_util.c-112-dt=(ir-nsteps + ir-init_step -
step)*time_per_step;
src/mdlib/sim_util.c-113-
src/mdlib/sim_util.c-114-if (dt = 300) {
src/mdlib/sim_util.c-115- finish = end+(time_t)dt;
src/mdlib/sim_util.c-116- sprintf(buf,%s,ctime(finish));
src/mdlib/sim_util.c-117- buf[strlen(buf)-1]='\0';
src/mdlib/sim_util.c-118- fprintf(out,, will finish %s,buf);
src/mdlib/sim_util.c-119-}
src/mdlib/sim_util.c-120-else
src/mdlib/sim_util.c-121- fprintf(out,, remaining runtime: %5d
s ,(int)dt);
src/mdlib/sim_util.c-122- fc = (int)dt / ir-nstlist;
src/mdlib/sim_util.c-123- fprintf(stderr, Fraction complete: %d \n,
fc);
src/mdlib/sim_util.c-124- }
src/mdlib/sim_util.c-125- if (gmx_parallel_env)
src/mdlib/sim_util.c-126-fprintf(out,\n);
src/mdlib/sim_util.c-127-
src/mdlib/sim_util.c-128- fflush(out);
src/mdlib/sim_util.c-129-}
Back Off! I just backed up md.edr to ./#md.edr.4#
starting mdrun 'Protein in water'
500 steps, 1.0 ps.
step 100, remaining runtime: 122 s Fraction complete: 0
step 200, remaining runtime:92 s Fraction complete: 0
On Thu, Sep 24, 2009 at 6:34 PM, Mark Abraham
mark.abra...@anu.edu.auwrote:
Jack Shultz wrote:
I figured out another way to update the progress of my simulation, but I
need to report the fraction of completion at the certain intervals of mdrun.
Possibly at every time step or if that does not make sense every 100
timesteps. I don't think this is a feature currently supported, so I will
have to make some source code chages. I am looking for the variables related
to total number of time steps and where it controls the the current time
step so I can calculate the fraction of complete where current-timestep /
total-timestep
Under at least some circumstances GROMACS writes the expected runtime
remaining to stderr, but I don't recall what/when. Piping that to some
useful script has to be a good start. You certainly don't need this data
every time step, and don't want to be perturbing mdrun to get it.
Even if the above was unsuitable, surely progress would only need to be
moderately accurate and for simulations that last many hours. If so, you'll
get good enough data by grepping a gmxdump of the .tpr to get the expected
frequencies of output and length of run, and then watching the growth of
whichever of .log/.trr/.edr is written most frequently. I/O buffering will
affect the numbers somewhat.
Mark
___
gmx-users mailing listgmx-users@gromacs.org
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Please search the archive at http://www.gromacs.org/search before
posting!
Please don't post (un)subscribe requests to the list. Use the www
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--
Jack
http://drugdiscoveryathome.com
http://hydrogenathome.org
--
Jack
http://drugdiscoveryathome.com
http://hydrogenathome.org
___
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
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Re: [gmx-users] timestep fraction complete
Thanks a bunch for the help Mark!
I made some additional changes that seem to work the way I need it.
src/mdlib/sim_util.c:122: fprintf(stderr, Fraction complete: %g\n,
(step - ir-init_step) / (float) ir-nsteps);
src/mdlib/sim_util.c-123-
src/mdlib/sim_util.c-124- f = fopen(progress.txt, w);
src/mdlib/sim_util.c-125- if (!f) return;
src/mdlib/sim_util.c-126- fprintf(f, %g, (step - ir-init_step) /
(float) ir-nsteps);
src/mdlib/sim_util.c-127- fclose(f);
src/mdlib/sim_util.c-128- }
On Thu, Sep 24, 2009 at 6:58 PM, Mark Abraham mark.abra...@anu.edu.auwrote:
Jack Shultz wrote:
I am hoping for an update every 10 minutes just to satisfy the anxieties
of volunteers crunching on my project, but every hour may be satisfactory.
And if I can do this without requiring any shell scripts it would be better
in my environment. So I started making some code modifications which
apparently did not work
src/mdlib/sim_util.c:93:void print_time(FILE *out,time_t start,int
step,t_inputrec *ir)
src/mdlib/sim_util.c-94-{
src/mdlib/sim_util.c-95- static real time_per_step;
src/mdlib/sim_util.c-96- static time_t end;
src/mdlib/sim_util.c-97- time_t finish;
src/mdlib/sim_util.c-98- double dt, fc;
src/mdlib/sim_util.c-99- char buf[48];
src/mdlib/sim_util.c-100- FILE *progress=progress.txt;
src/mdlib/sim_util.c-101-
src/mdlib/sim_util.c-102- if (!gmx_parallel_env)
src/mdlib/sim_util.c-103-fprintf(out,\r);
src/mdlib/sim_util.c-104- fprintf(out,step %d,step);
src/mdlib/sim_util.c-105- if ((step = ir-nstlist)) {
src/mdlib/sim_util.c-106-if ((ir-nstlist == 0) || ((step %
ir-nstlist) == 0)) {
src/mdlib/sim_util.c-107- /* We have done a full cycle let's update
time_per_step */
src/mdlib/sim_util.c-108- end=time(NULL);
src/mdlib/sim_util.c-109- dt=difftime(end,start);
src/mdlib/sim_util.c-110- time_per_step=dt/(step - ir-init_step +
1);
src/mdlib/sim_util.c-111-}
src/mdlib/sim_util.c-112-dt=(ir-nsteps + ir-init_step -
step)*time_per_step;
src/mdlib/sim_util.c-113-
src/mdlib/sim_util.c-114-if (dt = 300) { src/mdlib/sim_util.c-115-
finish = end+(time_t)dt;
src/mdlib/sim_util.c-116- sprintf(buf,%s,ctime(finish));
src/mdlib/sim_util.c-117- buf[strlen(buf)-1]='\0';
src/mdlib/sim_util.c-118- fprintf(out,, will finish %s,buf);
src/mdlib/sim_util.c-119-}
src/mdlib/sim_util.c-120-else
src/mdlib/sim_util.c-121- fprintf(out,, remaining runtime: %5d s
,(int)dt);
src/mdlib/sim_util.c-122- fc = (int)dt / ir-nstlist;
src/mdlib/sim_util.c-123- fprintf(stderr, Fraction complete: %d \n,
fc);
You're doing integer division and writing an integer. That won't get you
fraction complete, even if the ratio of dt (the remaining runtime in
seconds) and ir-nstlist (the number of steps between neighboursearches)
meant anything! Use
fprintf(stderr, Fraction complete: %g\n, (step - ir-init_step) / (float)
ir-nsteps);
Mark
src/mdlib/sim_util.c-124- }
src/mdlib/sim_util.c-125- if (gmx_parallel_env)
src/mdlib/sim_util.c-126-fprintf(out,\n);
src/mdlib/sim_util.c-127-
src/mdlib/sim_util.c-128- fflush(out);
src/mdlib/sim_util.c-129-}
Back Off! I just backed up md.edr to ./#md.edr.4#
starting mdrun 'Protein in water'
500 steps, 1.0 ps.
step 100, remaining runtime: 122 s Fraction complete: 0
step 200, remaining runtime:92 s Fraction complete: 0
On Thu, Sep 24, 2009 at 6:34 PM, Mark Abraham
mark.abra...@anu.edu.aumailto:
mark.abra...@anu.edu.au wrote:
Jack Shultz wrote:
I figured out another way to update the progress of my
simulation, but I need to report the fraction of completion at
the certain intervals of mdrun. Possibly at every time step or
if that does not make sense every 100 timesteps. I don't think
this is a feature currently supported, so I will have to make
some source code chages. I am looking for the variables related
to total number of time steps and where it controls the the
current time step so I can calculate the fraction of complete
where current-timestep / total-timestep
Under at least some circumstances GROMACS writes the expected
runtime remaining to stderr, but I don't recall what/when. Piping
that to some useful script has to be a good start. You certainly
don't need this data every time step, and don't want to be
perturbing mdrun to get it.
Even if the above was unsuitable, surely progress would only need to
be moderately accurate and for simulations that last many hours. If
so, you'll get good enough data by grepping a gmxdump of the .tpr to
get the expected frequencies of output and length of run, and then
watching the growth of whichever of .log/.trr/.edr is written most
frequently. I/O buffering will affect the numbers somewhat.
Mark
Re: [gmx-users] Limit mdrun runtime
So if I do this within a perl script, I will need to capture the pid and kill that process if it runs over 5 minutes? I'll try the -maxh first. Otherwise I'll spend some time trying to debug it. On Mon, Sep 14, 2009 at 11:09 AM, Berk Hess g...@hotmail.com wrote: If mdrun hangs -maxh won't help. You can kill mdrun using the kill command. But since mdrun catches signals, you might need kill -9 (the 'KILL' signal). Berk Date: Mon, 14 Sep 2009 10:56:43 -0400 From: jalem...@vt.edu To: gmx-users@gromacs.org Subject: Re: [gmx-users] Limit mdrun runtime Jack Shultz wrote: Hello, I have developed a workflow for prepping structures. One problem I have is sometimes it gets hung up on mdrun. Are there any mdrun parameters we can use to kill this process if it runs too long? The parameters we are using should not run over 5 minutes. I have not figured out how to do this with my script, but I guess there may be a way using SIGALRM. mdrun -maxh -Justin -- Jack http://drugdiscoveryathome.com http://hydrogenathome.org ___ 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/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/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- Express yourself instantly with MSN Messenger! MSN Messengerhttp://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/ ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- Jack http://drugdiscoveryathome.com http://hydrogenathome.org ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] Limit mdrun runtime
I think I found a sample code that does this actually
my $timeout = 180;
my $pid = fork;
if ( defined $pid ) {
if ( $pid ) {
# this is the parent process
local $SIG{ALRM} = sub { die TIMEOUT };
alarm 180;
# wait until child returns or timeout occurs
eval {
waitpid( $pid, 0 );
};
alarm 0;
if ( $@ $@ =~ m/TIMEOUT/ ) {
# timeout, kill the child process
kill 9, $pid;
}
}
else {
# this is the child process
# this call will never return. Note the use of exec instead of system
exec simulator --shell;
}
}
else {
die Could not fork.;
}
On Mon, Sep 14, 2009 at 11:56 AM, Jack Shultz
j...@drugdiscoveryathome.com wrote:
So if I do this within a perl script, I will need to capture the pid and kill
that process if it runs over 5 minutes? I'll try the -maxh first. Otherwise
I'll spend some time trying to debug it.
On Mon, Sep 14, 2009 at 11:09 AM, Berk Hess g...@hotmail.com wrote:
If mdrun hangs -maxh won't help.
You can kill mdrun using the kill command.
But since mdrun catches signals, you might need kill -9 (the 'KILL' signal).
Berk
Date: Mon, 14 Sep 2009 10:56:43 -0400
From: jalem...@vt.edu
To: gmx-users@gromacs.org
Subject: Re: [gmx-users] Limit mdrun runtime
Jack Shultz wrote:
Hello,
I have developed a workflow for prepping structures. One problem I have
is sometimes it gets hung up on mdrun. Are there any mdrun parameters we
can use to kill this process if it runs too long? The parameters we are
using should not run over 5 minutes. I have not figured out how to do
this with my script, but I guess there may be a way using SIGALRM.
mdrun -maxh
-Justin
--
Jack
http://drugdiscoveryathome.com
http://hydrogenathome.org
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--
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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Express yourself instantly with MSN Messenger! MSN Messenger
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--
Jack
http://drugdiscoveryathome.com
http://hydrogenathome.org
--
Jack
http://drugdiscoveryathome.com
http://hydrogenathome.org
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[gmx-users] Limit mdrun runtime
Hello, I have developed a workflow for prepping structures. One problem I have is sometimes it gets hung up on mdrun. Are there any mdrun parameters we can use to kill this process if it runs too long? The parameters we are using should not run over 5 minutes. I have not figured out how to do this with my script, but I guess there may be a way using SIGALRM. -- Jack http://drugdiscoveryathome.com http://hydrogenathome.org ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] Ligand Receptor
Hello, I'm trying to figure out how I can merge the ligand and receptor files. I used this script to prep a ligand I treated with GAFF perl amb2gmx.pl --prmtop test1.prmtop --crd test1.inpcrd --outname ligand This results in ligand.top ligand.gro Then I prepped a receptor pdb2gmx_d -f fzd2.pdb -ff amber03 -o conf.pdb Is there some way to merge these structures and then simulate with gromacs? -- Jack http://drugdiscoveryathome.com http://hydrogenathome.org ligand.top Description: Binary data ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] Re: Ligand Receptor
This is neat! Thanks http://code.google.com/p/acpypi/wiki/TutorialAcpypi4Gromacs On Fri, Jun 26, 2009 at 9:36 AM, Alanalanwil...@gmail.com wrote: Hi there, How about taking a look at acpypi.googlecode.com and its wikis? I hope it can help you. Alan On Fri, Jun 26, 2009 at 14:27, gmx-users-requ...@gromacs.org wrote: Hello, I'm trying to figure out how I can merge the ligand and receptor files. I used this script to prep a ligand I treated with GAFF perl amb2gmx.pl --prmtop test1.prmtop --crd test1.inpcrd --outname ligand This results in ligand.top ligand.gro Then I prepped a receptor pdb2gmx_d -f fzd2.pdb -ff amber03 -o conf.pdb Is there some way to merge these structures and then simulate with gromacs? -- Jack http://drugdiscoveryathome.com http://hydrogenathome.org -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. http://www.bio.cam.ac.uk/~awd28 ___ gmx-users mailing list gmx-us...@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- Jack http://drugdiscoveryathome.com http://hydrogenathome.org ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] How to build a lipid bilayer in GROMACS?
I don't know if this helps you, but there is a membrane plugin for VMD which you can download for free. I've used this to insert proteins in membranes and then use namd to run MD. I don't know what steps are involved to make this structure compatible with GROMACS. http://www.ks.uiuc.edu/Research/vmd/plugins/membrane/ On Sat, May 2, 2009 at 7:46 AM, Anirban Ghosh anirban...@yahoo.co.in wrote: Hi ALL, I have a protein pdb file. I want to put this protein molecule in a lipid bilayer using GROMACS. I shall be glad if anyone can kindly tell me how to build a lipid bilayer in GROMACS and how to embed the protein in it to get the final pdb of the entire system. Thanks a lot. Regards, Anirban Ghosh Grade Based Engineer Bioinformatics Team Scientific Engineering Computing Group Centre for Development of Advanced Computing Pune, India Anirban Ghosh Grade Based Engineer Bioinformatics Team Centre for Development of Advanced Computing (C-DAC) Pune, India Cricket on your mind? Visit the ultimate cricket website. Enter now! ___ gmx-users mailing list gmx-us...@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- Jack http://www.facebook.com/home.php#/profile.php?id=832713248 http://hydrogenathome.org ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] Reducing Size of Data
Hi, I am taking a look at reducing the size of my analysis. I've decreased log writing intervals. I notice mdruns generate these pdb files. Is there any way of reducing the frequency these files are written? I think that will go a long way to making my analysis easier. 05/02/2009 07:34 PM 155,211 eiwit.pdb 05/02/2009 07:43 PM 8,251,350 step117b.pdb 05/02/2009 07:44 PM 8,251,361 step117c.pdb 05/02/2009 07:38 PM 8,251,350 step20b.pdb 05/02/2009 07:38 PM 8,251,361 step20c.pdb 05/02/2009 07:38 PM 8,251,350 step27b.pdb 05/02/2009 07:38 PM 8,251,361 step27c.pdb 05/02/2009 07:40 PM 8,251,350 step79b.pdb 05/02/2009 07:40 PM 8,251,361 step79c.pdb 05/02/2009 07:40 PM 8,251,350 step80b.pdb 05/02/2009 07:41 PM 8,251,361 step80c.pdb 05/02/2009 07:41 PM 8,251,350 step91b.pdb 05/02/2009 07:41 PM 8,251,361 step91c.pdb 05/02/2009 07:41 PM 8,251,350 step92b.pdb 05/02/2009 07:42 PM 8,251,361 step92c.pdb 05/02/2009 07:42 PM 8,251,350 step93b.pdb 05/02/2009 07:42 PM 8,251,361 step93c.pdb 05/02/2009 07:42 PM 8,251,350 step94b.pdb 05/02/2009 07:42 PM 8,251,361 step94c.pdb 05/02/2009 07:42 PM 8,251,350 step96b.pdb 05/02/2009 07:43 PM 8,251,361 step96c.pdb -- Jack http://www.facebook.com/home.php#/profile.php?id=832713248 http://hydrogenathome.org ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] Prepping Docking Complexes
Hi Guys, Thanks for previous help. Especially Justin. I got the amber03 and tip3 water models working through my BOINC project now. But if I want to simulate a docking complex, I'm running to some errors preparing it. I have not done extensive research on this yet, but I'm wondering how I can prep these ligand-receptor complexes so they are acceptable to pdb2gmx. Maybe someone can point me in the right direction? --- Program pdb2gmx_d, VERSION 4.0.3 Source code file: pdb2gmx.c, line: 893 Fatal error: Chain identifier 'B' was used in two non-sequential blocks (residue 975, atom 7970) --- Workunit information http://hydrogenathome.org/result.php?resultid=1412984 Original complex http://hydrogenathome.org/sample_results/2559_1uwq_1238414317.pdb.tar.gz -- Jack http://www.facebook.com/home.php#/profile.php?id=832713248 http://hydrogenathome.org ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] Missing atom in residue
Hi, What are some of the ways used to fix these problems? Do you manually manipulate these files to add missing residues or are there any automated methods? I tried ignoring it with -missing, which is probably a bad way to treat this error. Still that did not ignore the error. Does this require a custom script for adding atoms? Atom CG not found in residue ARG94 while adding hydrogens -- Jack http://www.facebook.com/home.php#/profile.php?id=832713248 http://hydrogenathome.org ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] Integrating with BOINC: failing at minimization
Hello, I've tried a couple ways of running the workshop tutorial with a different protein and amber03 force field. It works with a clean install of gromacs, but I am trying to integrate it into a grid computing project. https://extras.csc.fi/chem/courses/gmx2007/tutorial1/tutorial1.pdf I tried several approaches to running this app but encountered a strange problem in both approaches to integrating. It always has trouble minimizing. This indicates to me, there is something strange with the environment that I created. If you have any hints for me that would be great. The two approaches I tried were: 1) putting all the dependent files in the same directory as the binary and executing it, this failed when I tested it stand alone and it created this same error 2) I tried writing a bash script to mimics the GMXRC.bash except it maps every directory relative to a temporary directory where everything runs. (e.g. GMXBIN=../slot/0/bin/) It seems to run fine through a workunit but then it does not minimize properly causing additional problems downstream Steepest Descents converged to machine precision in 54 steps, but did not reach the requested Fmax 10. Potential Energy = -8.35030867755191e+214 Maximum force = 7.83437759695905e+221 on atom 25439 Norm of force = 5.13628303396235e+219 http://www.hydrogenathome.org/result.php?resultid=1341858 -- Jack http://www.facebook.com/home.php#/profile.php?id=832713248 http://hydrogenathome.org ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] not referencing ffamber03.hdb
Hello, I have been trying to figure out why I'm getting this message. I looked over this site http://chemistry.csulb.edu/ffamber/index.html#usage But could not figure out why I'm getting this error. I'm running pdb2gmx_d.exe -ff amber03 WARNING: atom H is missing in residue LYSH 124 in the pdb file You might need to add atom H to the hydrogen database of residue LYSH in the file ff???.hdb (see the manual) WARNING: atom HA is missing in residue LYSH 124 in the pdb file You might need to add atom HA to the hydrogen database of residue LYSH in the file ff???.hdb (see the manual) WARNING: atom HB1 is missing in residue LYSH 124 in the pdb file You might need to add atom HB1 to the hydrogen database of residue LYSH in the file ff???.hdb (see the manual) -- Jack http://www.facebook.com/home.php#/profile.php?id=832713248 http://hydrogenathome.org ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] Range checking error: only on double precision
Hello, I just wanted to compare results between single and double precision. I reused the same parameters. Single works. Double caused errors on mdrun. Any idea why? http://hydrogenathome.org/result.php?resultid=1292662 --- Program mdrun, VERSION 4.0.3 Source code file: nsgrid.c, line: 357 Range checking error: Explanation: During neighborsearching, we assign each particle to a grid based on its coordinates. If your system contains collisions or parameter errors that give particles very high velocities you might end up with some coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot put these on a grid, so this is usually where we detect those errors. Make sure your system is properly energy-minimized and that the potential energy seems reasonable before trying again. Variable ci has value -2147483648. It should have been within [ 0 .. 300 ] -- Jack http://www.facebook.com/home.php#/profile.php?id=832713248 http://hydrogenathome.org ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] Range checking error: only on double precision
Justin, Can you suggest any pdb files I could use that are more simple? I've been trying to use files from tutorials but it seems like are always problematic. Jack On Tue, Mar 17, 2009 at 7:20 PM, Justin A. Lemkul jalem...@vt.edu wrote: Jack Shultz wrote: Hello, I just wanted to compare results between single and double precision. I reused the same parameters. Single works. Double caused errors on mdrun. Any idea why? http://hydrogenathome.org/result.php?resultid=1292662 I don't know why any of that worked at all. You've got missing atoms and inconsistent naming (LYSH should be LYP if you really want a protonated lysine under the Amber ports, etc). Did you give pdb2gmx -missing? Otherwise, topology generation should have failed. Especially troublesome: System has non-zero total charge: -2.309866e+01 I would suggest running tests on a physically realistic system that has all atoms present and an integer charge. Maybe single precision somehow overcame these topology problems, but I wouldn't trust any of the results. -Justin --- Program mdrun, VERSION 4.0.3 Source code file: nsgrid.c, line: 357 Range checking error: Explanation: During neighborsearching, we assign each particle to a grid based on its coordinates. If your system contains collisions or parameter errors that give particles very high velocities you might end up with some coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot put these on a grid, so this is usually where we detect those errors. Make sure your system is properly energy-minimized and that the potential energy seems reasonable before trying again. Variable ci has value -2147483648. It should have been within [ 0 .. 300 ] -- Justin A. Lemkul Graduate Research Assistant ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing list gmx-us...@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- Jack http://www.facebook.com/home.php#/profile.php?id=832713248 http://hydrogenathome.org ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] Range checking error: only on double precision
I guess its the amber03 force field I'm having issues with. The lysozyme tutorial works if I use -ff G43a2 Thanks Jack On Tue, Mar 17, 2009 at 8:01 PM, Justin A. Lemkul jalem...@vt.edu wrote: Well, several tutorials use lysozyme, PDB 1AKI. I would also recommend not using ffamber if you are running automated tests, since there are quirks with requiring specific nomenclature (for lysine, histidine, terminal residues, etc). -Justin Jack Shultz wrote: Justin, Can you suggest any pdb files I could use that are more simple? I've been trying to use files from tutorials but it seems like are always problematic. Jack On Tue, Mar 17, 2009 at 7:20 PM, Justin A. Lemkul jalem...@vt.edu wrote: Jack Shultz wrote: Hello, I just wanted to compare results between single and double precision. I reused the same parameters. Single works. Double caused errors on mdrun. Any idea why? http://hydrogenathome.org/result.php?resultid=1292662 I don't know why any of that worked at all. You've got missing atoms and inconsistent naming (LYSH should be LYP if you really want a protonated lysine under the Amber ports, etc). Did you give pdb2gmx -missing? Otherwise, topology generation should have failed. Especially troublesome: System has non-zero total charge: -2.309866e+01 I would suggest running tests on a physically realistic system that has all atoms present and an integer charge. Maybe single precision somehow overcame these topology problems, but I wouldn't trust any of the results. -Justin --- Program mdrun, VERSION 4.0.3 Source code file: nsgrid.c, line: 357 Range checking error: Explanation: During neighborsearching, we assign each particle to a grid based on its coordinates. If your system contains collisions or parameter errors that give particles very high velocities you might end up with some coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot put these on a grid, so this is usually where we detect those errors. Make sure your system is properly energy-minimized and that the potential energy seems reasonable before trying again. Variable ci has value -2147483648. It should have been within [ 0 .. 300 ] -- Justin A. Lemkul Graduate Research Assistant ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing list gmx-us...@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing list gmx-us...@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- Jack http://www.facebook.com/home.php#/profile.php?id=832713248 http://hydrogenathome.org ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] Minimization not converging
Hi, I think that my minimization are not running long enough. I've been following the parameters in tutorials but it seems like they all die at 34 steps I've been using these tutorials https://extras.csc.fi/chem/courses/gmx2007/tutorial1/tutorial1.pdf http://md.chem.rug.nl/education/mdcourse/MDpract.html Its been the same case for me regardless to whether I use Windows or Linux platforms. Are there settings I can use to make the simulation minimize longer or is this case where I need to have double precision version? -- Jack http://www.facebook.com/home.php#/profile.php?id=832713248 http://hydrogenathome.org ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] Re: Minimization not converging
I should have included some output Step= 32, Dmax= 2.4e-06 nm, Epot= -1.03223e+05 Fmax= 3.87326e+06, atom= 25439 Step= 33, Dmax= 1.2e-06 nm, Epot= -1.03222e+05 Fmax= 3.87334e+06, atom= 25439 Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax 10 Double precision normally gives you higher accuracy. You might need to increase your constraint accuracy, or turn off constraints alltogether (set constraints = none in mdp file) writing lowest energy coordinates. Steepest Descents converged to machine precision in 34 steps, but did not reach the requested Fmax 10. Potential Energy = -1.4354568e+06 Maximum force = 6.9535597e+10 on atom 25439 Norm of force = 4.5592896e+08 More details here. http://www.hydrogenathome.org/result.php?resultid=1291344 On Thu, Mar 12, 2009 at 10:59 AM, Jack Shultz jshu...@hydrogenathome.org wrote: Hi, I think that my minimization are not running long enough. I've been following the parameters in tutorials but it seems like they all die at 34 steps I've been using these tutorials https://extras.csc.fi/chem/courses/gmx2007/tutorial1/tutorial1.pdf http://md.chem.rug.nl/education/mdcourse/MDpract.html Its been the same case for me regardless to whether I use Windows or Linux platforms. Are there settings I can use to make the simulation minimize longer or is this case where I need to have double precision version? -- Jack http://www.facebook.com/home.php#/profile.php?id=832713248 http://hydrogenathome.org -- Jack http://www.facebook.com/home.php#/profile.php?id=832713248 http://hydrogenathome.org ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] Reducing Size of Data
Hi, I was wondering if there are any ways to reduce the amount of data produce or compact it better. On some of my runs mdruns I ran out of the default disk space BOINC allocated for my file system to run this analysis. If I use the -compact flag, does that affect the size of the trajectory files? -- Jack http://www.facebook.com/home.php#/profile.php?id=832713248 http://hydrogenathome.org ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] redirect md.log to standard ourput
I'm trying to capture errors when I run simulations through boinc. Is there a way to redirect the log to the standard output? -- Jack http://www.facebook.com/home.php#/profile.php?id=832713248 http://hydrogenathome.org ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] redirect md.log to standard ourput
ok thanks, if it becomes critical to troubleshooting, I'll just get my hands dirty with the cpp code. On Wed, Mar 11, 2009 at 1:01 PM, Mark Abraham mark.abra...@anu.edu.auwrote: Jack Shultz wrote: I'm trying to capture errors when I run simulations through boinc. Is there a way to redirect the log to the standard output? Not with the existing implementation. The result would be a confusing mess of the existing stdout and the .log file, anyway. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- Jack http://www.facebook.com/home.php#/profile.php?id=832713248 http://hydrogenathome.org ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] mdrun dies with STATUS_ACCESS_VIOLATION
Has anyone come across this error on a windows platform? Any suggestions? I ran it through a BOINC workunit then tried it stand-alone for troubleshooting. It produces the same result. 23 [main] mdrun 4084 _cygtls::handle_exceptions: Exception: STATUS_ACCESS_VIOLATION 316870 [main] mdrun 4084 open_stackdumpfile: Dumping stack trace to mdrun.exe.stackdump Here are the details http://hydrogenathome.org/result.php?resultid=1290554 -- Jack http://www.facebook.com/home.php#/profile.php?id=832713248 http://hydrogenathome.org ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] Re: mdrun dies with STATUS_ACCESS_VIOLATION
Also the dump file contains this information Exception: STATUS_ACCESS_VIOLATION at eip=0044C09B eax=000533A4 ebx=0045 ecx=000528B4 edx=7F956C88 esi=FD6A65C0 edi=7F5D6C88 ebp=7FB40020 esp=0022AE30 program=C:\Documents and Settings\All Users\Application Data\BOINC\slots\0\gromacs\bin\mdrun.exe, pid 2396, thread main cs=001B ds=0023 es=0023 fs=003B gs= ss=0023 Stack trace: Frame Function Args 7FB40020 0044C09B (, , , ) End of stack trace On Wed, Mar 11, 2009 at 9:25 PM, Jack Shultz jshu...@hydrogenathome.org wrote: Has anyone come across this error on a windows platform? Any suggestions? I ran it through a BOINC workunit then tried it stand-alone for troubleshooting. It produces the same result. 23 [main] mdrun 4084 _cygtls::handle_exceptions: Exception: STATUS_ACCESS_VIOLATION 316870 [main] mdrun 4084 open_stackdumpfile: Dumping stack trace to mdrun.exe.stackdump Here are the details http://hydrogenathome.org/result.php?resultid=1290554 -- Jack http://www.facebook.com/home.php#/profile.php?id=832713248 http://hydrogenathome.org -- Jack http://www.facebook.com/home.php#/profile.php?id=832713248 http://hydrogenathome.org ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] mdrun dies with STATUS_ACCESS_VIOLATION
Thank you, now I'm testing this on a 64 bit, robust linux box. I was using the parameters from this tutorial https://extras.csc.fi/chem/courses/gmx2007/tutorial1/tutorial1.pdf One other question, if GROMACS was compiled with single precision, would that make a difference regarding how well it minimizes a system? On Wed, Mar 11, 2009 at 10:24 PM, Mark Abraham mark.abra...@anu.edu.au wrote: Jack Shultz wrote: Has anyone come across this error on a windows platform? Any suggestions? I ran it through a BOINC workunit then tried it stand-alone for troubleshooting. It produces the same result. 23 [main] mdrun 4084 _cygtls::handle_exceptions: Exception: STATUS_ACCESS_VIOLATION 316870 [main] mdrun 4084 open_stackdumpfile: Dumping stack trace to mdrun.exe.stackdump Here are the details http://hydrogenathome.org/result.php?resultid=1290554 The GROMACS issue is in the few lines above this. See http://wiki.gromacs.org/index.php/Errors#1-4_interaction_not_within_cut-off As Justin said, you should simplify your problem by getting a system on which a trustworthy version of GROMACS works correctly, before confounding your problem with your other issues. Mark ___ gmx-users mailing list gmx-us...@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- Jack http://www.facebook.com/home.php#/profile.php?id=832713248 http://hydrogenathome.org ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] Cuda support
Has anyone used these binaries? How are they? Any recommendations on using GPUs? https://simtk.org/project/xml/downloads.xml?group_id=161#package_id600 -- Jack http://www.facebook.com/home.php#/profile.php?id=832713248 http://hydrogenathome.org ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] Re: gmx-users Digest, Vol 59, Issue 58
Yes I read somewhere that treating the simulation space as a cube has some drawbacks. I'll try these parameters. On Mon, Mar 9, 2009 at 3:36 PM, Andrew Voronkov drugdes...@yandex.ru wrote: I've used this tutorial: https://extras.csc.fi/chem/courses/gmx2007/tutorial1/tutorial1.pdf I've used command line: editconf -c -f conf.gro -bt dodecahedron -d 0.7 -o box.gro to center the protein, but the problem remains - protein is still in the edge of the water box. There is also 1-4 warning for which I see no reasons and very fast presision reached time. Steepest Descents: Tolerance (Fmax) = 1.0e+01 Number of steps = 200 Warning: 1-4 interaction between 2 and 21 at distance 6.197 which is larger than the 1-4 table size 2.000 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file or with user tables increase the table size Step= 14, Dmax= 1.2e-06 nm, Epot= 2.82932e+24 Fmax= inf, atom= 4 Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax 10 Double precision normally gives you higher accuracy. You might need to increase your constraint accuracy, or turn off constraints alltogether (set constraints = none in mdp file) writing lowest energy coordinates. Steepest Descents converged to machine precision in 15 steps, but did not reach the requested Fmax 10. Potential Energy = 2.8293175e+24 Maximum force = inf on atom 4 Norm of force = inf gcq#239: killing children ... (Insight/Parasoft) and...@linux-f29d:~/GROMACS_MD/FZD1 Here are MDP files: EM.mdp integrator = steep nsteps = 200 nstlist = 10 rlist = 1.0 coulombtype = pme rcoulomb = 1.0 vdw-type = cut-off rvdw = 1.0 nstenergy = 10 constraints = none integrator = md nsteps = 2500 dt = 0.002 nstlist = 10 rlist = 1.0 coulombtype = pme rcoulomb = 1.0 vdw-type = cut-off rvdw = 1.0 tcoupl = Berendsen tc-grps = protein non-protein tau-t = 0.1 0.1 ref-t = 298 298 Pcoupl = Berendsen tau-p = 1.0 compressibility = 5e-5 5e-5 5e-5 0 0 0 ref-p = 1.0 nstenergy = 100 define = -DPOSRES Best regards, Andrew -- Message: 3 Date: Fri, 06 Mar 2009 13:41:28 -0500 From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] .gro files problems To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 49b16e58.3000...@vt.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed Andrew Voronkov wrote: Dear GROMACS users, I'm trying to do this tutorial It's always best to post a link to the tutorial you're using. There are dozens of Gromacs tutorials out there. with 1ijy structure from rcsb.org All .gro files on different step raise questions. 1) conf.gro - by VMD I see some strange groups which are not linked with the protein. This may or may not be an artefact of VMD's efforts to guess where bonds should be. Sometimes it's smart, sometimes it's not. 2) After solvatation step in solvated.gro the protein is not in the middle of solution but somewhere in the edge, how to solve this? editconf -c 3) After energy minimization protein even goes out of the solution. Looks like I am doing everything according to the tutorial (except the structure) but there are still problems... Use editconf -c and try again. The .gro files are in the attachment. The listserv ate them, but they probably won't aid much in diagnosis, anyway. On minimization step I also get: Steepest Descents converged to machine precision in 73 steps, but did not reach the requested Fmax Depending on what your target Fmax was, this may not be a problem. Fmax 1000 is generally adequate for a simple protein in water. On equilibration step I also get an error(with such .gro file it very proabable): Or you could have an error in your .mdp file (inappropriate parameters, etc), so if things continue to fail, post the .mdp file (not as an attachment, just embed the text). -Justin ___ gmx-users mailing list gmx-us...@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- Jack http://www.facebook.com/home.php#/profile.php?id=832713248 http://hydrogenathome.org ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to
[gmx-users] visualizing trajectories real-time
I'm wondering if there are any GPL or GNU applications I can use to visualize simulations. I would like to integrate the code into a screen saver for my distributed computing project. -- Jack http://hydrogenathome.org ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] Formating PDB Files
Hello, I am experimenting with formatting pdb files using pdb2gmx. Currently I am downloading ligand files from RCSB.ORG. These are non-protein pdb files. When I look at their residues, instead of having a standard residue, they use their pdb id as the residue id. pdb2gmx does not like this because these are not standard residues. Is there a setting I can use to make pdb2gmx to ignore this? Otherwise I can use a sed command to replace all instances of a given residue name. However, when I try replacing with a standard residue name, I still run into errors. Here is an example ligand pdb file http://www.rcsb.org/pdb/files/ligand/002_ideal.pdb Notice instead of having a standard residue it uses 002 ATOM 1 C1 002 A 1 -1.036 0.293 0.447 1.00 10.00 C ATOM 2 C2 002 A 1 -1.041 1.804 0.685 1.00 10.00 C ATOM 3 C3 002 A 1 -2.288 2.191 1.482 1.00 10.00 C Any advice? Does GROMACS only support the standard 20 amino acids? -- Jack ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] Support of Saddle Point Calculations
Thank you David, I am about halfway through the Gromacs 2007 Workshop material. Very nice. I'm wondering if there is any workshop videos covering QM/MM methods in Gromacs. Thanks, Jack On Sun, Oct 19, 2008 at 4:14 PM, David van der Spoel [EMAIL PROTECTED]wrote: Jack Shultz wrote: Hello, I am fairly new to GROMACS but I have spent time running tutorials for several other molecular dynamics applications. I would like to know if the current framework for GROMACS has support for methods that calculate saddle point energy in first-order reactions. If so, are there examples I can read about? First, GROMACS does not support reactions, unless you use the QM/MM methods in which case you have to look into e.g. Gaussian's way of doing a Transition State optimization. Second, you can do normal mode analysis which would give you indirectly the needed information, if you have a conformation that you know is the transition state. Jack ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David van der Spoel, Ph.D., Professor of Biology Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [EMAIL PROTECTED][EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Support of Saddle Point Calculations
Hello, I am fairly new to GROMACS but I have spent time running tutorials for several other molecular dynamics applications. I would like to know if the current framework for GROMACS has support for methods that calculate saddle point energy in first-order reactions. If so, are there examples I can read about? Jack ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
