[gmx-users] Replica Exchange with GPUs
Dear users, I'm currently doing some experiments with the implicit solvation model running on GPUs with GROMACS. I can make simple (conventional MD) simulations using the GPUs, allowing great acceleration by using 1 GPU. However, I was wondering about how to make Replica Exchange Molecular Dynamics (REMD) with the GPUs. I suppose each GPU can be used to run a replica, is this possible? thanks in advance, Leandro Bortot -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] g_clustsize
Dear Justin, Thank you very much from your help. I think that I should work more on this command and will ask you next. I don't know why does it bother me for it's .xvg and -tu !!! Thank you very much again. Best Regards Sara On 7/19/12 9:42 AM, mohammad agha wrote: > Dear Justin, > > Thank you very much from your response. > according you said I should set -cut with less than 0.7, but this doesn't > answer me! I didn't say that, but your results are completely consistent with what I said about how g_clustsize is working and the output it is producing. > for 0.6: > 0.00e+00 115 > 6.00e+01 107 > 1.20e+02 114 > 1.80e+02 105 > 2.40e+02 100 > 3.00e+02 96 > 3.60e+02 103 > 4.20e+02 111 > 4.80e+02 99 > > > for 0.5 > 0.00e+00 139 > 6.00e+01 135 > 1.20e+02 136 > 1.80e+02 136 > 2.40e+02 140 > 3.00e+02 139 > 3.60e+02 142 > 4.20e+02 138 > 4.80e+02 137 > As you decrease the value of -cut, you get more and more "clusters" (which largely contain only one molecule). I suppose if you want a count of monomers (which is the opposite of what g_clustsize does) then you could try setting -cut to zero, but I don't know if this will even work. The code may expect a non-zero cutoff value. -Justin > > Can you help me about this, Please? > Best Regards > Sara > > >> >> >> >> >> Dear Gromacs Users, >> >> I have several questions about g_clustsize, Please help me. >> I have several micelles in my system and I want to calculate: the number of >> monomers in micelles and cluster number and monomer number during the time >> of simulation, I used from this command as is follows: >> g_clustsize -f clustered.xtc -s c.tpr -tu us -mol -cut 0.7 -nc nclust.xvg >> -ac avclust.xvg -mc maxclust.xvg >> I have 150 monomer initially in my system. I selected -cut from rdf.xvg for >> tail-tail that 0.7 was the first minimum in this graph. >> >> >> >> >> 1- the nclust.xvg file is as follows: >> @ title "Number of clusters" >> @ xaxis label "Time (us)" >> @ yaxis label "N" >> @TYPE xy >> 0.00e+00 104 >> 6.00e+01 88 >> 1.20e+02 89 >> 1.80e+02 85 >> 2.40e+02 79 >> 3.00e+02 79 >> 3.60e+02 91 >> 4.20e+02 89 >> . . . . . .. . .. . .. . .. ... . >> >> . . ... . .. .. .. . . .. . .. .. >> >> . . ... . . . . ... . >> whereas in the first step of simulation there is no cluster and it should be >> 0!!! >> > > You've set the cutoff value to 0.7 nm, so any molecules with contacts within > this distance will be considered clustered. Out of 150 monomers, some are > within this distance in the starting frame. Note that with 104 clusters, the > majority of your 150 monomers are basically in individual clusters. > >> >> 2- when I choose -tu (ps, ms, us , ... ) there is no difference among them >> about time either file .xvg and graphs!!!why and where is problem? > > This is odd. The code indicates that you should be able to display whatever > units you choose. In any case, you should determine from the trajectory what > the interval (in ps) is and plot accordingly. Time units can always be > manipulated after the fact with simple multiplication or division operations. > >> 3- how should I find the number of monomers from first to end of simulation >> that it should be 150 in the first step. >> > > Probably not with g_clustsize. It does exactly the opposite, but perhaps you > can back-calculate the results using a combination of output files. It's not > immediately clear to me how you would do that, though. Perhaps someone else > can > comment. > > -Justin > -- Justin A. Lemkul, Ph.D. Research Scientist 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 * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] g_clustsize
On 7/19/12 9:42 AM, mohammad agha wrote: Dear Justin, Thank you very much from your response. according you said I should set -cut with less than 0.7, but this doesn't answer me! I didn't say that, but your results are completely consistent with what I said about how g_clustsize is working and the output it is producing. for 0.6: 0.00e+00 115 6.00e+01 107 1.20e+02 114 1.80e+02 105 2.40e+02 100 3.00e+02 96 3.60e+02 103 4.20e+02 111 4.80e+02 99 for 0.5 0.00e+00 139 6.00e+01 135 1.20e+02 136 1.80e+02 136 2.40e+02 140 3.00e+02 139 3.60e+02 142 4.20e+02 138 4.80e+02 137 As you decrease the value of -cut, you get more and more "clusters" (which largely contain only one molecule). I suppose if you want a count of monomers (which is the opposite of what g_clustsize does) then you could try setting -cut to zero, but I don't know if this will even work. The code may expect a non-zero cutoff value. -Justin Can you help me about this, Please? Best Regards Sara Dear Gromacs Users, I have several questions about g_clustsize, Please help me. I have several micelles in my system and I want to calculate: the number of monomers in micelles and cluster number and monomer number during the time of simulation, I used from this command as is follows: g_clustsize -f clustered.xtc -s c.tpr -tu us -mol -cut 0.7 -nc nclust.xvg -ac avclust.xvg -mc maxclust.xvg I have 150 monomer initially in my system. I selected -cut from rdf.xvg for tail-tail that 0.7 was the first minimum in this graph. 1- the nclust.xvg file is as follows: @title "Number of clusters" @xaxis label "Time (us)" @yaxis label "N" @TYPE xy 0.00e+00 104 6.00e+01 88 1.20e+02 89 1.80e+02 85 2.40e+02 79 3.00e+02 79 3.60e+02 91 4.20e+02 89 . . . . . .. . .. . .. . .. ... . . . ... . .. .. .. . . .. . .. .. . . ... . . . . ... . whereas in the first step of simulation there is no cluster and it should be 0!!! You've set the cutoff value to 0.7 nm, so any molecules with contacts within this distance will be considered clustered. Out of 150 monomers, some are within this distance in the starting frame. Note that with 104 clusters, the majority of your 150 monomers are basically in individual clusters. 2- when I choose -tu (ps, ms, us , ... ) there is no difference among them about time either file .xvg and graphs!!!why and where is problem? This is odd. The code indicates that you should be able to display whatever units you choose. In any case, you should determine from the trajectory what the interval (in ps) is and plot accordingly. Time units can always be manipulated after the fact with simple multiplication or division operations. 3- how should I find the number of monomers from first to end of simulation that it should be 150 in the first step. Probably not with g_clustsize. It does exactly the opposite, but perhaps you can back-calculate the results using a combination of output files. It's not immediately clear to me how you would do that, though. Perhaps someone else can comment. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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 * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] g_clustsize
Dear Justin, Thank you very much from your response. according you said I should set -cut with less than 0.7, but this doesn't answer me! for 0.6: 0.00e+00 115 6.00e+01 107 1.20e+02 114 1.80e+02 105 2.40e+02 100 3.00e+02 96 3.60e+02 103 4.20e+02 111 4.80e+02 99 for 0.5 0.00e+00 139 6.00e+01 135 1.20e+02 136 1.80e+02 136 2.40e+02 140 3.00e+02 139 3.60e+02 142 4.20e+02 138 4.80e+02 137 Can you help me about this, Please? Best Regards Sara > > > > > Dear Gromacs Users, > > I have several questions about g_clustsize, Please help me. > I have several micelles in my system and I want to calculate: the number of > monomers in micelles and cluster number and monomer number during the time of > simulation, I used from this command as is follows: > g_clustsize -f clustered.xtc -s c.tpr -tu us -mol -cut 0.7 -nc nclust.xvg -ac > avclust.xvg -mc maxclust.xvg > I have 150 monomer initially in my system. I selected -cut from rdf.xvg for > tail-tail that 0.7 was the first minimum in this graph. > > > > > 1- the nclust.xvg file is as follows: > @ title "Number of clusters" > @ xaxis label "Time (us)" > @ yaxis label "N" > @TYPE xy > 0.00e+00 104 > 6.00e+01 88 > 1.20e+02 89 > 1.80e+02 85 > 2.40e+02 79 > 3.00e+02 79 > 3.60e+02 91 > 4.20e+02 89 > . . . . . .. . .. . .. . .. ... . > > . . ... . .. .. .. . . .. . .. .. > > . . ... . . . . ... . > whereas in the first step of simulation there is no cluster and it should be > 0!!! > You've set the cutoff value to 0.7 nm, so any molecules with contacts within this distance will be considered clustered. Out of 150 monomers, some are within this distance in the starting frame. Note that with 104 clusters, the majority of your 150 monomers are basically in individual clusters. > > 2- when I choose -tu (ps, ms, us , ... ) there is no difference among them > about time either file .xvg and graphs!!!why and where is problem? This is odd. The code indicates that you should be able to display whatever units you choose. In any case, you should determine from the trajectory what the interval (in ps) is and plot accordingly. Time units can always be manipulated after the fact with simple multiplication or division operations. > 3- how should I find the number of monomers from first to end of simulation > that it should be 150 in the first step. > Probably not with g_clustsize. It does exactly the opposite, but perhaps you can back-calculate the results using a combination of output files. It's not immediately clear to me how you would do that, though. Perhaps someone else can comment. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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 * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: Water molecules cannot be settled, why?
On 19/07/2012 6:52 PM, Ladasky wrote: Tsjerk Wassenaar wrote Hi John, Check where the unsettling water molecule is placed. If it's in the protein. that may be the cause of the problem. Otherwise, it's some of the other stuff you're doing, but rule out the simple things first. Thank you Tsjerk. I posted a reply several days ago, and I tried again earlier today. My first attempt appeared in the email digest but not on this web page. My second attempt hasn't appeared, and I expect that my ISP is responsible (Yahoo started attaching ads to email signatures, which might set off spam filters). I'm now posting directly from Nabble. I looked at two different simulations which crashed. The unsettled water molecules appear to be far from the protein in all cases. Tentatively, then, I would conclude that my protein is fine, because the errors are not occurring in atoms which are proximal to the protein. Instead, I suspect there is something wrong with my protocol. But here are the details, so you can check my reasoning. You can try a vacuum simulation on your solute if you want a further test of whether its topology and starting configuration is OK. As the details of the protocol in the last message that I posted showed, I'm using five CPU cores for my simulations. So the domain decomposition in mdrun is 5 x 1 x 1. When the simulations crash, the error handling routine outputs only the domain which contains the unsettled water molecule. In the first simulation that I examined, the domain was all solvent. No protein atoms were present. The crash occurred on step 81,240 of my final molecular dynamics run, and the atom that was identified as a problem was number 45191. So I looked at the two PDB files that were dumped, and searched for atom 45191. I think that the first file describes the system immediately before the crash, and the second file shows the results of the bad calculations, am I correct? Different phases of the constraint algorithm, at least. Perhaps as you say - one would have to read the code. Here is a selected portion of each file, showing atom 45191 and its neighbors: step81240b_n4.pdb ATOM 41009 OW SOL 1 74.590 46.654 65.507 ATOM 41010 HW1 SOL 1 74.580 47.272 66.294 ATOM 41011 HW2 SOL 1 73.700 46.205 65.425 ATOM 43679 OW SOL 1 71.579 49.011 70.894 ATOM 43680 HW1 SOL 1 71.730 49.197 69.924 ATOM 43681 HW2 SOL 1 71.013 49.735 71.288 ATOM 45191 OW SOL 1 72.656 46.524 71.131 ATOM 45192 HW1 SOL 1 72.614 45.938 70.322 ATOM 45193 HW2 SOL 1 72.389 47.455 70.883 ATOM 6926 OW SOL 1 75.926 46.701 73.317 ATOM 6927 HW1 SOL 1 75.024 46.674 72.886 ATOM 6928 HW2 SOL 1 76.564 47.194 72.724 ATOM 16016 OW SOL 1 73.244 51.473 72.961 ATOM 16017 HW1 SOL 1 73.712 51.310 72.092 ATOM 16018 HW2 SOL 1 73.472 52.387 73.296 step81240c_n4.pdb ATOM 41009 OW SOL 1 74.582 46.669 65.502 ATOM 41010 HW1 SOL 1 74.582 47.320 66.260 ATOM 41011 HW2 SOL 1 73.689 46.221 65.445 ATOM 43679 OW SOL 1-66321836.00084864872.00046148104.000 ATOM 43680 HW1 SOL 1 71.706 49.216 69.937 ATOM 43681 HW2 SOL 1 1085546624.000-1490344960.000-271069120.000 ATOM 45191 OW SOL 1-176865.797532401.250-1222093.250 ATOM 45192 HW1 SOL 119264928.000-53927836.000125858544.000 ATOM 45193 HW2 SOL 1 72.351 47.488 70.877 ATOM 6926 OW SOL 1 75.925 46.703 73.302 ATOM 6927 HW1 SOL 1 75.021 46.680 72.875 ATOM 6928 HW2 SOL 1 76.562 47.196 72.710 ATOM 16016 OW SOL 1 73.240 51.478 72.957 ATOM 16017 HW1 SOL 1 73.728 51.296 72.103 ATOM 16018 HW2 SOL 1 73.442 52.407 73.266 WOW. Something went seriously wrong with four atoms in that step. Are those even coordinates? For some reason, atom 45191 was selected as the one to trigger the crash report. I looked through the whole PDB file for other problems, and I found one more oxygen atom in another water molecule which had similarly wild coordinates. It was half-way across the domain, not even a neighbor of atom 45191. I had a look at atom 45191 in PyMol, and there was nothing obviously wrong with its position right before the crash. Stereo image here: http://www.flickr.com/photos/15579975@N00/7553843726/ In the second crashed simulation, only a single abnormal atom was found in the PDB file. The domain containing that water molecule did contain a part of the protein, but the water molecule was far from the protein. Here's an image of that domain (unsettled water molecule marked with an amber sphere): http://www.flickr.com/photos/15579975@N00/7554770182/ All right, so what could be wrong with my protocols? Since my problems began, I have made exactly four changes that I can see: 1) I have upgraded from G
Re: [gmx-users] g_clustsize
On 7/19/12 8:06 AM, mohammad agha wrote: Dear Gromacs Users, I have several questions about g_clustsize, Please help me. I have several micelles in my system and I want to calculate: the number of monomers in micelles and cluster number and monomer number during the time of simulation, I used from this command as is follows: g_clustsize -f clustered.xtc -s c.tpr -tu us -mol -cut 0.7 -nc nclust.xvg -ac avclust.xvg -mc maxclust.xvg I have 150 monomer initially in my system. I selected -cut from rdf.xvg for tail-tail that 0.7 was the first minimum in this graph. 1- the nclust.xvg file is as follows: @title "Number of clusters" @xaxis label "Time (us)" @yaxis label "N" @TYPE xy 0.00e+00 104 6.00e+01 88 1.20e+02 89 1.80e+02 85 2.40e+02 79 3.00e+02 79 3.60e+02 91 4.20e+02 89 . . . . . .. . .. . .. . .. ... . . . ... . .. .. .. . . .. . .. .. . . ... . . . . ... . whereas in the first step of simulation there is no cluster and it should be 0!!! You've set the cutoff value to 0.7 nm, so any molecules with contacts within this distance will be considered clustered. Out of 150 monomers, some are within this distance in the starting frame. Note that with 104 clusters, the majority of your 150 monomers are basically in individual clusters. 2- when I choose -tu (ps, ms, us , ... ) there is no difference among them about time either file .xvg and graphs!!!why and where is problem? This is odd. The code indicates that you should be able to display whatever units you choose. In any case, you should determine from the trajectory what the interval (in ps) is and plot accordingly. Time units can always be manipulated after the fact with simple multiplication or division operations. 3- how should I find the number of monomers from first to end of simulation that it should be 150 in the first step. Probably not with g_clustsize. It does exactly the opposite, but perhaps you can back-calculate the results using a combination of output files. It's not immediately clear to me how you would do that, though. Perhaps someone else can comment. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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 * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] g_clustsize
Dear Gromacs Users, I have several questions about g_clustsize, Please help me. I have several micelles in my system and I want to calculate: the number of monomers in micelles and cluster number and monomer number during the time of simulation, I used from this command as is follows: g_clustsize -f clustered.xtc -s c.tpr -tu us -mol -cut 0.7 -nc nclust.xvg -ac avclust.xvg -mc maxclust.xvg I have 150 monomer initially in my system. I selected -cut from rdf.xvg for tail-tail that 0.7 was the first minimum in this graph. 1- the nclust.xvg file is as follows: @ title "Number of clusters" @ xaxis label "Time (us)" @ yaxis label "N" @TYPE xy 0.00e+00 104 6.00e+01 88 1.20e+02 89 1.80e+02 85 2.40e+02 79 3.00e+02 79 3.60e+02 91 4.20e+02 89 . . . . . .. . .. . .. . .. ... . . . ... . .. .. .. . . .. . .. .. . . ... . . . . ... . whereas in the first step of simulation there is no cluster and it should be 0!!! 2- when I choose -tu (ps, ms, us , ... ) there is no difference among them about time either file .xvg and graphs!!!why and where is problem? 3- how should I find the number of monomers from first to end of simulation that it should be 150 in the first step. May I ask you to help me, Please? Thank you in advance. Best Regards Sara -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] g_clustsize
Dear Gromacs Users, I have several questions about g_clustsize, Please help me. I have several micelles in my system and I want to calculate: the number of monomers in micelles and cluster number and monomer number during the time of simulation, I used from this command as is follows: g_clustsize -f clustered.xtc -s c.tpr -tu us -mol -cut 0.7 -nc nclust.xvg -ac avclust.xvg -mc maxclust.xvg I have 150 monomer initially in my system. I selected -cut from rdf.xvg for tail-tail that 0.7 was the first minimum in this graph. 1- the nclust.xvg file is as follows: @ title "Number of clusters" @ xaxis label "Time (us)" @ yaxis label "N" @TYPE xy 0.00e+00 104 6.00e+01 88 1.20e+02 89 1.80e+02 85 2.40e+02 79 3.00e+02 79 3.60e+02 91 4.20e+02 89 . . . . . .. . .. . .. . .. ... . . . ... . .. .. .. . . .. . .. .. . . ... . . . . ... . whereas in the first step of simulation there is no cluster and it should be 0!!! 2- when I choose -tu (ps, ms, us , ... ) there is no difference among them about time either file .xvg and graphs!!!why and where is problem? 3- how should I find the number of monomers from first to end of simulation that it should be 150 in the first step. May I ask you to help me, Please? Thank you in advance. Best Regards Sara -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] question about pdb2gmx
On 7/19/12 6:28 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: There is only one Cystein: ATOM 1797 N CYS A 211 10.568 1.888 4.891 1.00 1.00 ATOM 1798 CA CYS A 211 11.782 1.312 5.391 1.00 1.00 ATOM 1799 CB CYS A 211 12.968 1.606 4.452 1.00 1.00 ATOM 1800 SG CYS A 211 14.599 1.282 5.172 1.00 1.00 ATOM 1801 C CYS A 211 12.106 1.904 6.723 1.00 1.00 ATOM 1802 O CYS A 211 12.427 1.169 7.655 1.00 1.00 As I said before, -ss allows you to choose whether cysteine is free or involved in a disulfide. With only one cysteine, there's nothing that -ss will do; there is no possibility for a disulfide. If you need an anionic cysteine, you need to use a force field that supports such a residue (Amber03 should) and name the residue accordingly (CYM). Otherwise, CYS will be a free cysteine with the normal protonated thiol. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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 * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] question about pdb2gmx
There is only one Cystein: ATOM 1797 N CYS A 211 10.568 1.888 4.891 1.00 1.00 ATOM 1798 CA CYS A 211 11.782 1.312 5.391 1.00 1.00 ATOM 1799 CB CYS A 211 12.968 1.606 4.452 1.00 1.00 ATOM 1800 SG CYS A 211 14.599 1.282 5.172 1.00 1.00 ATOM 1801 C CYS A 211 12.106 1.904 6.723 1.00 1.00 ATOM 1802 O CYS A 211 12.427 1.169 7.655 1.00 1.00 Eva > > > On 7/19/12 6:17 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: >> Hi Justin, >> thank you for your answer. >> I already tried the -ss command but nothing happens. The program just >> writes the topology file but it does not ask me anything. My command >> was: >> >> pdb2gmx -f protOnly.pdb -o 3m71.gro -p 3m71.top -ss -water tip3p -ff >> amber03 >> >> is there something wrong with this command? > > No, it's fine. How many cysteines are in the structure? > > -Justin > > -- > > > Justin A. Lemkul, Ph.D. > Research Scientist > 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 > * Only plain text messages are allowed! > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] question about pdb2gmx
On 7/19/12 6:17 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: Hi Justin, thank you for your answer. I already tried the -ss command but nothing happens. The program just writes the topology file but it does not ask me anything. My command was: pdb2gmx -f protOnly.pdb -o 3m71.gro -p 3m71.top -ss -water tip3p -ff amber03 is there something wrong with this command? No, it's fine. How many cysteines are in the structure? -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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 * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] question about pdb2gmx
Hi Justin, thank you for your answer. I already tried the -ss command but nothing happens. The program just writes the topology file but it does not ask me anything. My command was: pdb2gmx -f protOnly.pdb -o 3m71.gro -p 3m71.top -ss -water tip3p -ff amber03 is there something wrong with this command? Best, Eva > > > On 7/19/12 5:00 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: >> Hi everybody, >> I want to add protonation states to my protein with pdb2gmx. >> I now that there are the options: >> >> -lys -arg -asp -glu -his >> >> to do this. >> >> But was is about the cystein. How can I protonate this one? >> Is there also an option for it which I haven't seen? >> > > The -ss flag controls cysteine protonation, in the sense that you can > toggle > between disulfide and free forms of cysteine. Some force fields include > an > anionic form of cysteine as well. > > -Justin > > -- > > > Justin A. Lemkul, Ph.D. > Research Scientist > 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 > * Only plain text messages are allowed! > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] question about pdb2gmx
On 7/19/12 5:00 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: Hi everybody, I want to add protonation states to my protein with pdb2gmx. I now that there are the options: -lys -arg -asp -glu -his to do this. But was is about the cystein. How can I protonate this one? Is there also an option for it which I haven't seen? The -ss flag controls cysteine protonation, in the sense that you can toggle between disulfide and free forms of cysteine. Some force fields include an anionic form of cysteine as well. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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 * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] question about pdb2gmx
Hi everybody, I want to add protonation states to my protein with pdb2gmx. I now that there are the options: -lys -arg -asp -glu -his to do this. But was is about the cystein. How can I protonate this one? Is there also an option for it which I haven't seen? Thank you , Eva -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: Water molecules cannot be settled, why?
Tsjerk Wassenaar wrote > > Hi John, > > Check where the unsettling water molecule is placed. If it's in the > protein. that may be the cause of the problem. Otherwise, it's some of > the other stuff you're doing, but rule out the simple things first. > > Thank you Tsjerk. I posted a reply several days ago, and I tried again earlier today. My first attempt appeared in the email digest but not on this web page. My second attempt hasn't appeared, and I expect that my ISP is responsible (Yahoo started attaching ads to email signatures, which might set off spam filters). I'm now posting directly from Nabble. I looked at two different simulations which crashed. The unsettled water molecules appear to be far from the protein in all cases. Tentatively, then, I would conclude that my protein is fine, because the errors are not occurring in atoms which are proximal to the protein. Instead, I suspect there is something wrong with my protocol. But here are the details, so you can check my reasoning. As the details of the protocol in the last message that I posted showed, I'm using five CPU cores for my simulations. So the domain decomposition in mdrun is 5 x 1 x 1. When the simulations crash, the error handling routine outputs only the domain which contains the unsettled water molecule. In the first simulation that I examined, the domain was all solvent. No protein atoms were present. The crash occurred on step 81,240 of my final molecular dynamics run, and the atom that was identified as a problem was number 45191. So I looked at the two PDB files that were dumped, and searched for atom 45191. I think that the first file describes the system immediately before the crash, and the second file shows the results of the bad calculations, am I correct? Here is a selected portion of each file, showing atom 45191 and its neighbors: step81240b_n4.pdb ATOM 41009 OW SOL 1 74.590 46.654 65.507 ATOM 41010 HW1 SOL 1 74.580 47.272 66.294 ATOM 41011 HW2 SOL 1 73.700 46.205 65.425 ATOM 43679 OW SOL 1 71.579 49.011 70.894 ATOM 43680 HW1 SOL 1 71.730 49.197 69.924 ATOM 43681 HW2 SOL 1 71.013 49.735 71.288 ATOM 45191 OW SOL 1 72.656 46.524 71.131 ATOM 45192 HW1 SOL 1 72.614 45.938 70.322 ATOM 45193 HW2 SOL 1 72.389 47.455 70.883 ATOM 6926 OW SOL 1 75.926 46.701 73.317 ATOM 6927 HW1 SOL 1 75.024 46.674 72.886 ATOM 6928 HW2 SOL 1 76.564 47.194 72.724 ATOM 16016 OW SOL 1 73.244 51.473 72.961 ATOM 16017 HW1 SOL 1 73.712 51.310 72.092 ATOM 16018 HW2 SOL 1 73.472 52.387 73.296 step81240c_n4.pdb ATOM 41009 OW SOL 1 74.582 46.669 65.502 ATOM 41010 HW1 SOL 1 74.582 47.320 66.260 ATOM 41011 HW2 SOL 1 73.689 46.221 65.445 ATOM 43679 OW SOL 1-66321836.00084864872.00046148104.000 ATOM 43680 HW1 SOL 1 71.706 49.216 69.937 ATOM 43681 HW2 SOL 1 1085546624.000-1490344960.000-271069120.000 ATOM 45191 OW SOL 1-176865.797532401.250-1222093.250 ATOM 45192 HW1 SOL 119264928.000-53927836.000125858544.000 ATOM 45193 HW2 SOL 1 72.351 47.488 70.877 ATOM 6926 OW SOL 1 75.925 46.703 73.302 ATOM 6927 HW1 SOL 1 75.021 46.680 72.875 ATOM 6928 HW2 SOL 1 76.562 47.196 72.710 ATOM 16016 OW SOL 1 73.240 51.478 72.957 ATOM 16017 HW1 SOL 1 73.728 51.296 72.103 ATOM 16018 HW2 SOL 1 73.442 52.407 73.266 WOW. Something went seriously wrong with four atoms in that step. Are those even coordinates? For some reason, atom 45191 was selected as the one to trigger the crash report. I looked through the whole PDB file for other problems, and I found one more oxygen atom in another water molecule which had similarly wild coordinates. It was half-way across the domain, not even a neighbor of atom 45191. I had a look at atom 45191 in PyMol, and there was nothing obviously wrong with its position right before the crash. Stereo image here: http://www.flickr.com/photos/15579975@N00/7553843726/ In the second crashed simulation, only a single abnormal atom was found in the PDB file. The domain containing that water molecule did contain a part of the protein, but the water molecule was far from the protein. Here's an image of that domain (unsettled water molecule marked with an amber sphere): http://www.flickr.com/photos/15579975@N00/7554770182/ All right, so what could be wrong with my protocols? Since my problems began, I have made exactly four changes that I can see: 1) I have upgraded from GROMACS 4.0 to 4.5. 2) I once used the -deuterate option in pdb2gmx, and I am presently trying to avoid it. I asked whether -deuterate has any effect on water molecules in a previous post, or only on the hydrogens in proteins. So far, I have not been made to understand that
Re: [gmx-users] 1replica/1cpu problem
Sorry for the multiple emails but everytime I tried to send the mail I obtained a message like this: "The message's content type was not explicitly allowed. Please send your messages as plain text only. See http://www.gromacs.org/Support/Mailing_Lists"; So I tried as long as no message has been replied to me. Concerning the bug fixes, I did the following steps git clone git://git.gromacs.org/gromacs.git gromacs-4.5.5-patches cd gromacs-4.5.5-patches git checkout --track -b release-4-5-patches origin/release-4-5-patches git pull ./bootstrap ./configure --prefix=/ibpc/etna/oteri/PKG/gromacs/4.5.5/patched --without-x --enable-mpi --program-suffix=_mpi --enable-all-static CFLAGS="-I/ibpc/etna/oteri/PKG/openmpi/1.4.5/include -I/ibpc/etna/oteri/PKG/fftw/3.3.1/gcc/include" "LDFLAGS=-L/ibpc/etna/oteri/PKG/fftw/3.3.1/gcc/lib -L/ibpc/etna/oteri/PKG/openmpi/1.4.5/lib" LIBSUFFIX=_mpi make mdrun make install-mdrun 2012/7/19 Mark Abraham : > On 19/07/2012 12:32 AM, francesco oteri wrote: >> >> Dear gromacs users, >> I am trying to run a replica exchange simulation using the files you find >> in http://dl.dropbox.com /u/40545409/gmx_mailinglist/inputs.tgz >> >> The 4 replicas have been generated, as following: >> grompp -p rest2.top -c 03md.gro -n index.ndx -o rest2_0 -f rest2_0.mdp >> grompp -p rest2.top -c 03md.gro -n index.ndx -o rest2_1 -f rest2_1.mdp >> grompp -p rest2.top -c 03md.gro -n index.ndx -o rest2_2 -f rest2_2.mdp >> grompp -p rest2.top -c 03md.gro -n index.ndx -o rest2_3 -f rest2_3.mdp >> >> The simulation was started with command, using gromacs 4.5.5 with the >> latest bug fix: > > > Which bug fix? How did you apply it? > > Mark > > >> mpirun -np 4 mdrun_mpi -s rest2_.tpr -multi 4 -replex 1000 >& out1 >> >> giving the following error: >> >> [etna:10799] *** An error occurred in MPI_comm_size >> [etna:10799] *** on communicator MPI_COMM_WORLD >> [etna:10799] *** MPI_ERR_COMM: invalid communicator >> [etna:10799] *** MPI_ERRORS_ARE_FATAL (your MPI job will now abort) >> -- >> mpirun has exited due to process rank 0 with PID 10796 on >> node etna exiting without calling "finalize". This may >> have caused other processes in the application to be >> terminated by signals sent by mpirun (as reported here). >> -- >> [etna:10795] 3 more processes have sent help message >> help-mpi-errors.txt / mpi_errors_are_fatal >> [etna:10795] Set MCA parameter "orte_base_help_aggregate" to 0 to see >> all help / error messages >> >> >> The nice thing is that the same error doesn't appear either if I use >> the 4.5.5 without applying tha patches!!! >> >> mpirun -np 4 mdrun_mpi -s rest2_.tpr -multi 4 -replex 1000 >& out2 >> >> or the bug fixed with multiple processors per replica: >> >> mpirun -np 8 mdrun_mpi -s rest2_.tpr -multi 4 -replex 1000 >& out3 >> >> Since I have to use more then 4 replicas, I need to run 1cpu/replica. >> >> Has someone any idea of the probem? >> >> Francesco > > > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Only plain text messages are allowed! > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the www > interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Cordiali saluti, Dr.Oteri Francesco -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
