[gmx-users] work calculation
Hi all, I want to calculate the work done of pulling one ligand through the channel. I have pulled the molecule through the channel and I have the pullx and pullf files. I saw one post regarding this in the mailing list, but it was not given a final solution. Can anyone help me? Thanks, -- Aswathy -- 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] PMF of ligand transport
Hi gromacs users, I am using Gromacs 4.0.4 package. I am doing SMD of a ligand transport through a channel. I performed SMD and did umbrella sampling (Thanks to Justin for his tutorial). Extracted frames with a window spacing interval of ~0.12nm. and did 1ns sampling. Histograms are with reasonabvle overlap. Then I used g_wham for plotting PMF considering first 300ps as equilibration. I am getting a plot , but potential is increasing constantly. ie, PMF is not converged as mentioned the tutorial? Do I need to extend the sampling ? or any other reason? Please help me. Thank you. -Aswathy -- 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] PMF of ligand transport
Ok i will explain you in detail. Initially i pulled the ligand through the protein channel , using the given parameters. pull = umbrella pull_geometry= distance pull_dim = N N Y pull_start = yes pull_nstxout = 10 pull_nstfout = 10 pull_ngroups = 1 pull_group0 = r_57 pull_group1 = r_C1 pull_rate1 = 0.01 pull_k1 = 1500 Then I extracted the frames from the trajectory using the perl program provided with tutorial. COM distance I took as nearly 0.12 nm. (But sometimes I failed to obtain frames exactly at that interval, but took nearly 0.12). Each frame I used for Umbrella sampling for 1ns. Then I checked histograms for overlapping (Some histograms were entirely overlapped and I removed that from the list, where ever gaps i selected new frames and did sampling so that I can get an evenly distributed histograms , I know this will change the overall COM distribution but is there any other way to solve this?) . Finally once I obtained reasonably good overlapped histograms, I plotted PMF using g_wham. The plot was a steeply increasing potential with some small curves here and there. The PMF is not at all converged. Did I made any mistake any where , I am confused. If you want I can attach the PMF profile Thank you. -Aswathy On Thu, May 6, 2010 at 12:56 PM, Jochen Hub wrote: > Aswathy wrote: > >> >> Hi gromacs users, >> >> I am using Gromacs 4.0.4 package. I am doing SMD of a ligand transport >> through a channel. >> >> I performed SMD and did umbrella sampling (Thanks to Justin for his >> tutorial). Extracted frames with a window spacing interval of ~0.12nm. and >> did 1ns sampling. Histograms are with reasonabvle overlap. Then I used >> g_wham for plotting PMF considering first 300ps as equilibration. >> > Isn't SMD usually referred to pulling at some finite pulling speed? That > would not be umbrella sampling. > > Anyway, you'll have to provide a lot more data to enable us to help you. > > Jochen > > > > >> I am getting a plot , but potential is increasing constantly. ie, PMF is >> not converged as mentioned the tutorial? Do I need to extend the sampling ? >> or any other reason? >> >> Please help me. >> Thank you. >> >> -Aswathy >> > > > -- > --- > Dr. Jochen Hub > Molecular Biophysics group > Dept. of Cell & Molecular Biology > Uppsala University. Box 596, 75124 Uppsala, Sweden. > Phone: +46-18-4714451 Fax: +46-18-511755 > --- > > -- > 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 > -- Aswathy -- 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] PMF of ligand transport
Can any one help me please? I looking forward to hear from any of you. Thank you. On Thu, May 6, 2010 at 1:19 PM, Aswathy wrote: > Ok i will explain you in detail. > > Initially i pulled the ligand through the protein channel , using the > given parameters. > > pull = umbrella > pull_geometry= distance > pull_dim = N N Y > pull_start = yes > pull_nstxout = 10 > pull_nstfout = 10 > pull_ngroups = 1 > pull_group0 = r_57 > pull_group1 = r_C1 > pull_rate1 = 0.01 > pull_k1 = 1500 > > Then I extracted the frames from the trajectory using the perl program > provided with tutorial. COM distance I took as nearly 0.12 nm. (But > sometimes I failed to obtain frames exactly at that interval, but took > nearly at 0.12). Each frame I used for Umbrella sampling for 1ns. > Then I checked histograms for overlapping (Some histograms were entirely > overlapped and I removed that from the list, where ever gaps i selected new > frames and did sampling so that I can get an evenly distributed histograms , > I know this will change the overall COM distribution but is there any other > way to solve this?) . > > Finally once I obtained reasonably good overlapped histograms, I plotted > PMF using g_wham. The plot was a steeply increasing potential. How can we > get increased PMF even when the ligand is reached out of the channel? > > Did I made any mistake any where , I am confused. > > Thank you. > -Aswathy > > > > On Thu, May 6, 2010 at 12:56 PM, Jochen Hub wrote: > >> Aswathy wrote: >> >>> >>> Hi gromacs users, >>> >>> I am using Gromacs 4.0.4 package. I am doing SMD of a ligand transport >>> through a channel. >>> >>> I performed SMD and did umbrella sampling (Thanks to Justin for his >>> tutorial). Extracted frames with a window spacing interval of ~0.12nm. and >>> did 1ns sampling. Histograms are with reasonabvle overlap. Then I used >>> g_wham for plotting PMF considering first 300ps as equilibration. >>> >> Isn't SMD usually referred to pulling at some finite pulling speed? That >> would not be umbrella sampling. >> >> Anyway, you'll have to provide a lot more data to enable us to help you. >> >> Jochen >> >> >> >> >>> I am getting a plot , but potential is increasing constantly. ie, PMF is >>> not converged as mentioned the tutorial? Do I need to extend the sampling ? >>> or any other reason? >>> >>> Please help me. >>> Thank you. >>> >>> -Aswathy >>> >> >> >> -- >> --- >> Dr. Jochen Hub >> Molecular Biophysics group >> Dept. of Cell & Molecular Biology >> Uppsala University. Box 596, 75124 Uppsala, Sweden. >> Phone: +46-18-4714451 Fax: +46-18-511755 >> ----------- >> >> -- >> 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 >> > > > > -- > Aswathy > -- Aswathy -- 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] PMF of ligand transport
Thanks for your reply. In this case reference (r57) is not the part of the channel. But it is a residue in the loop above the channel entry. Thats why I used pull_geometry=distance. Therefore I am pulling the ligand away from this reference. Thanks -Aswathy On Mon, May 10, 2010 at 3:05 PM, Thomas Piggot wrote: > Hi, > > If you defined the reference (r_57) as part of your channel then with > pull_geometry=distance you will have problems as the distance between > pull_group1 and pull_group0 becomes closer to zero and then the distance > becomes positive again. > > I recently had this with my umbrella sampling simulations. Search for the > discussion of things you can do to address this issue on the list. To stop > this being a problem in the first place you should have used > pull_geometry=position. > > Cheers > > Tom > > Aswathy wrote: > >> Can any one help me please? I looking forward to hear from any of you. >> Thank you. >> >> >> On Thu, May 6, 2010 at 1:19 PM, Aswathy > ammasa...@gmail.com>> wrote: >> >>Ok i will explain you in detail. >> >> Initially i pulled the ligand through the protein channel , using >>the given parameters. >> >>pull = umbrella >>pull_geometry= distance >>pull_dim = N N Y >>pull_start = yes >>pull_nstxout = 10 >>pull_nstfout = 10 >>pull_ngroups = 1 >>pull_group0 = r_57 >>pull_group1 = r_C1 >>pull_rate1 = 0.01 >>pull_k1 = 1500 >> >>Then I extracted the frames from the trajectory using the perl >>program provided with tutorial. COM distance I took as nearly 0.12 >>nm. (But sometimes I failed to obtain frames exactly at that >>interval, but took nearly at 0.12). Each frame I used for Umbrella >>sampling for 1ns. >>Then I checked histograms for overlapping (Some histograms were >>entirely overlapped and I removed that from the list, where ever >>gaps i selected new frames and did sampling so that I can get an >>evenly distributed histograms , I know this will change the overall >>COM distribution but is there any other way to solve this?) . >> >>Finally once I obtained reasonably good overlapped histograms, I >>plotted PMF using g_wham. The plot was a steeply increasing >>potential. How can we get increased PMF even when the ligand is >>reached out of the channel? >> >> >> >>Did I made any mistake any where , I am confused. >> >>Thank you. >>-Aswathy >> >> >> >>On Thu, May 6, 2010 at 12:56 PM, Jochen Hub ><mailto:joc...@xray.bmc.uu.se>> wrote: >> >>Aswathy wrote: >> >> >>Hi gromacs users, >> >>I am using Gromacs 4.0.4 package. I am doing SMD of a ligand >>transport through a channel. >> >>I performed SMD and did umbrella sampling (Thanks to Justin >>for his tutorial). Extracted frames with a window spacing >>interval of ~0.12nm. and did 1ns sampling. Histograms are >>with reasonabvle overlap. Then I used g_wham for plotting >>PMF considering first 300ps as equilibration. >> >>Isn't SMD usually referred to pulling at some finite pulling >> speed? That would not be umbrella sampling. >> >>Anyway, you'll have to provide a lot more data to enable us to >>help you. >> >>Jochen >> >> >> >> >>I am getting a plot , but potential is increasing >>constantly. ie, PMF is not converged as mentioned the >>tutorial? Do I need to extend the sampling ? or any other >>reason? >> >>Please help me. >>Thank you. >> >>-Aswathy >> >> >> >>-- --- >>Dr. Jochen Hub >>Molecular Biophysics group >>Dept. of Cell & Molecular Biology >>Uppsala University. Box 596, 75124 Uppsala, Sweden. >>Phone: +46-18-4714451 Fax: +46-18-511755 >> --- >> >>-- gmx-users mailing listgmx-users@gromacs.org >><mailto:gmx-users@gromacs.org> >> >>
Re: [gmx-users] PMF of ligand transport
I am pulling through the channel with respect to a single residue on one "side"(extracellular) of the structure. I have used pull_geometry = distance & pull_dim = N N Y. From this what I understood is ligand will pull along the z direction with respect to the reference group (away from r_57). (i.e from extracellular to intracellular). Is this correct? Here is my umbrella sampling .mdp parameters pull = umbrella pull_geometry= distance pull_dim = N N Y pull_start = yes pull_nstxout = 10 pull_nstfout = 10 pull_ngroups = 1 pull_group0 = r_57 pull_group1 = r_C1 pull_k1 = 1000 pull_init1 = 0 On Mon, May 10, 2010 at 4:50 PM, Justin A. Lemkul wrote: > > > Aswathy wrote: > >> Thanks for your reply. >> >> In this case reference (r57) is not the part of the channel. But it is a >> residue in the loop above the channel entry. Thats why I used >> pull_geometry=distance. Therefore I am pulling the ligand away from this >> reference. >> >> > So you are not pulling through the channel? Or you are pulling through the > channel with respect to a single residue on one "side" of the structure? If > your ligand ever crosses over this reference in any way, the reference > distance will change sign and thus Tom is right, you should use > "pull_geometry = position." With "distance," you can only ever have > positive reference distances. > > What are your .mdp settings during umbrella sampling? > > -Justin > > Thanks >> -Aswathy >> >> >> On Mon, May 10, 2010 at 3:05 PM, Thomas Piggot > t.pig...@soton.ac.uk>> wrote: >> >>Hi, >> >>If you defined the reference (r_57) as part of your channel then >>with pull_geometry=distance you will have problems as the distance >>between pull_group1 and pull_group0 becomes closer to zero and then >>the distance becomes positive again. >> >>I recently had this with my umbrella sampling simulations. Search >>for the discussion of things you can do to address this issue on the >>list. To stop this being a problem in the first place you should >>have used pull_geometry=position. >> >>Cheers >> >>Tom >> >>Aswathy wrote: >> >>Can any one help me please? I looking forward to hear from any >>of you. >>Thank you. >> >> >>On Thu, May 6, 2010 at 1:19 PM, Aswathy ><mailto:ammasa...@gmail.com> <mailto:ammasa...@gmail.com >> >><mailto:ammasa...@gmail.com>>> wrote: >> >> Ok i will explain you in detail. >> >>Initially i pulled the ligand through the protein channel , >>using >> the given parameters. >> >> pull = umbrella >> pull_geometry= distance >> pull_dim = N N Y >> pull_start = yes >> pull_nstxout = 10 >> pull_nstfout = 10 >> pull_ngroups = 1 >> pull_group0 = r_57 >> pull_group1 = r_C1 >> pull_rate1 = 0.01 >> pull_k1 = 1500 >> >> Then I extracted the frames from the trajectory using the perl >> program provided with tutorial. COM distance I took as nearly >>0.12 >> nm. (But sometimes I failed to obtain frames exactly at that >> interval, but took nearly at 0.12). Each frame I used for >>Umbrella >> sampling for 1ns. >> Then I checked histograms for overlapping (Some histograms were >> entirely overlapped and I removed that from the list, where ever >> gaps i selected new frames and did sampling so that I can get an >> evenly distributed histograms , I know this will change the >>overall >> COM distribution but is there any other way to solve this?) . >> >> Finally once I obtained reasonably good overlapped histograms, I >> plotted PMF using g_wham. The plot was a steeply increasing >> potential. How can we get increased PMF even when the ligand is >> reached out of the channel? >> >> >>Did I made any mistake any where , I am confused. >> >>
Re: [gmx-users] PMF of ligand transport
On Mon, May 10, 2010 at 6:29 PM, Justin A. Lemkul wrote: > Ok . Now I understood. I have one more doubt , as I mentioned to you, I am > using one residue in the extracellular loop as a reference point. Since this > is in the loop, do you think it can be good reference point (due to th large > fluctuatuion in the loop, will it affect the result)? > > Aswathy wrote: > >> I am pulling through the channel with respect to a single residue on one >> "side"(extracellular) of the structure. I have used pull_geometry = distance >> & pull_dim = N N Y. From this what I understood is ligand will pull along >> the z direction with respect to the reference group (away from r_57). (i.e >> from extracellular to intracellular). Is this correct? >> >> > I don't think so. If you are pulling through a channel, using an > extracellular residue as a reference, you will be changing the sign of the > distance, rendering "pull_geometry = distance" useless. For example, in > order to properly calculate the PMF, you have to pull from the aqueous > solvent, into the channel, then back out into the solvent. At some point, > your ligand is outside the channel (such that, for example, the z-coordinate > of the ligand is greater than that of r_57, so distance > 0). Then, as your > ligand enters the channel, its z-coordinate is less than that of r_57, so > distance < 0. If this is the case, you must use "pull_geometry = position" > to get the correct signs, otherwise your umbrella sampling window reference > distances will be nonsensical. > > -Justin > > Here is my umbrella sampling .mdp parameters >> >> pull = umbrella >> pull_geometry= distance >> pull_dim = N N Y >> pull_start = yes >> pull_nstxout = 10 >> pull_nstfout = 10 >> pull_ngroups = 1 >> pull_group0 = r_57 >> pull_group1 = r_C1 >> pull_k1 = 1000 >> pull_init1 = 0 >> >> On Mon, May 10, 2010 at 4:50 PM, Justin A. Lemkul > jalem...@vt.edu>> wrote: >> >> >> >>Aswathy wrote: >> >>Thanks for your reply. >> >> In this case reference (r57) is not the part of the channel. >>But it is a residue in the loop above the channel entry. Thats >>why I used pull_geometry=distance. Therefore I am pulling the >>ligand away from this reference. >> >> >>So you are not pulling through the channel? Or you are pulling >>through the channel with respect to a single residue on one "side" >>of the structure? If your ligand ever crosses over this reference >>in any way, the reference distance will change sign and thus Tom is >>right, you should use "pull_geometry = position." With "distance," >>you can only ever have positive reference distances. >> >>What are your .mdp settings during umbrella sampling? >> >>-Justin >> >>Thanks >>-Aswathy >> >> >>On Mon, May 10, 2010 at 3:05 PM, Thomas Piggot >>mailto:t.pig...@soton.ac.uk> >><mailto:t.pig...@soton.ac.uk <mailto:t.pig...@soton.ac.uk>>> >> wrote: >> >> Hi, >> >> If you defined the reference (r_57) as part of your channel then >> with pull_geometry=distance you will have problems as the >>distance >> between pull_group1 and pull_group0 becomes closer to zero >>and then >> the distance becomes positive again. >> >> I recently had this with my umbrella sampling simulations. >> Search >> for the discussion of things you can do to address this issue >>on the >> list. To stop this being a problem in the first place you should >> have used pull_geometry=position. >> >> Cheers >> >> Tom >> >> Aswathy wrote: >> >> Can any one help me please? I looking forward to hear >>from any >> of you. >> Thank you. >> >> >> On Thu, May 6, 2010 at 1:19 PM, Aswathy >>mailto:ammasa...@gmail.com> >> <mailto:ammasa...@gmail.com <mailto:ammasa...@gmail.com>> >><mailto:ammasa...@gmail.com <mailto:ammasa...@gmail.com> >> >>
Re: [gmx-users] Re: PMF of ligand transport
Hi Justin, I am sorry, i dint understand this point "Your problem was only related to the actual umbrella sampling itself." ? You meant I just want to repeat umbrella sampling only? In order to further understand that "Distance " problem, May I ask one more question,( please ignore if its a stupid one..) As Thomas suggested, = is the channel and x the dummy and l the ligand x l = later time x ==l== If this is the case, then there wont be sign problem with "distance", right??? (Once again forgive me if I am wrong, because I know you already put your maximum effort to make me understand this thing) And if we use a dummy particle, will the movement of that particle will also matter ? How can we fix that? Thank you. Aswathy On Mon, May 10, 2010 at 8:45 PM, Thomas Schlesier wrote: > Would it be possible to use a dummy particle near the entrance of the > channel? = is the channel and x the dummy and l the ligand > x l = > later time > x ==l== > Give the dummy no charge and zero lj-parameters and construt the position > form the atoms at the entry of the channel. > I think it will be important that the dummy is farther away from the > channel then your ligand, else you will get problem with the distance > geometry (because the distance changes the sign). > The other important thing is that the box is long enough that the distance > between the dummy and your ligand is always smaller then half the box > vector, or else the distance goes wrong. > > (My first idea was to use the entrance area of the channel as the > reference, but then there would be the problems with the sign-changing of > the distance -> so the idea with the dummy particle). > > Greetings > Thomas > > > > > > Aswathy wrote: > > > > > > Thank you very much for all replies. > > > > > > No w I just want to try SMd with geometry type as position . But one > > > thing is still confusing me, ie; reference group. > > > > > If you have already generated a suitable set of positions from which you > have > generated umbrella sampling windows, you do not need to repeat the SMD. > Your > problem was only related to the actual umbrella sampling itself. > > > > I have the ligand in the solvent (at the mouth of the > > > channel(extracellular).) Now I want to pull this ligand to the > > > intracellular solvent through the channel. My understanding is that the > > > reference group should be the in the same direction of the channel(ie, > > > at the intracellular end of the channel), so that if I use "position", > > > the ligand should move towards the reference group (Please correct me > if > > > this wrong). i have only solvent at this end(end of the channel) . Can > I > > > set water molecules as reference point? or any molecule at this > > > intracellular end is fine? > > > > > In theory, you can set whatever you want, but if those water molecules > diffuse, > then you're trying to hit a rapidly-moving target! Always choose a > relatively > static part of the structure in the direction you want to pull. > > -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 > -- Aswathy -- 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] PMF of ligand transport
Hi Chris, Thank you very much for your detailed mail. Now I have a doubt on this pull_init parameter. i read your previous posts regarding this, but still have a confusion. My query is that for each configuration when I run umbrella sampling, will this pull_init value needs to change?(I suppose so, if its true how?) When it should be negative and positive? Could you please explain this. Thanks for your valuable time Thanks & Regards, Aswathy On Mon, May 10, 2010 at 9:55 PM, Chris Neale wrote: > Pick a small collection of backbone atoms near the center of your channel > and use them as your reference group. Overcome the sign problem by optimal > selection of pull options (see below). pull_pbcatom values should not be > important > if you select your groups as I suggest -- otherwise be sure to understand > how they work. > > > ; COM PULLING > pull = umbrella > pull_geometry= position > pull_dim = N N Y > pull_start = no > pull_nstxout = 250 > pull_nstfout = 250 > pull_ngroups = 1 > pull_group0 = MY_SELECTION_OF_BACKBONE_ATOMS > pull_pbcatom0= 0 > pull_group1 = LIGAND > pull_pbcatom1= 0 > pull_init1 = 0 0 THISDIST > pull_rate1 = 0 > pull_k1 = 500.0 > pull_vec1= 0 0 0 > > Chris. > > -- original message -- > > I think Justin meant that you have various positions of the ligand in the > channel (from the SMD), so you don't need to make a new run to determine new > positions in the channel. You need only new umbrella sampling simulations. > > Yep, the movement of the particle will also matter, because if the particle > moves much on the z-axis, the distance between the particle and the ligand > will change. So you would want the particle fixed relative to the channel. > Two ideas: > Place the particle above the entrance of the channel. Pick three atoms from > the entrance of the channel and determine the distance between the atoms and > the particle. Then use distance_restraints or constraints with a > 'bondlength' equal to the measured distance. If everything goes right the > particle would stay where you placed it, since it does not interact with the > enviroment it should not really influence your simulation (only through the > constraints or distance_restraints). > I don't now how big your system is, but it would probably be a good idea to > make a short test simulation, to look if the particle changes the system > behavior. > But it's only an idea, i hope other people comment it. > > Greetings > Thomas > > > -- > 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 > -- Aswathy -- 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] PMF of ligand transport
Chris, I understand, Sorry for that . Actually I mixed up the concept of SteeredMd with umbrella sampling. So I was confused whenever you people gave suggestions. Now I thing I got the idea , Thanks for you people. I will try myself and see. Thanks once again. -Aswathy On Tue, May 11, 2010 at 6:48 PM, wrote: > It represents a difference in coordinate space. You'll get the most out of > this list if you continue to try to solve your problems before posting and > avoid submitting every question/problem that you hit upon under a > continuously in-use title. Did you try it and look at you -px output file? I > suggest that you do some tutorials. Also, set up a test system and pull two > water molecules apart within a box of water and use VMD to see what happens. > Then try a slightly more difficult test system... these are the types of > things that worked for me. > > pull_init1 = 0 0 -5 > pull_init1 = 0 0 -4.9 > pull_init1 = 0 0 -4.8 > ... > pull_init1 = 0 0 4.9 > pull_init1 = 0 0 5 > > But it's up to you to determine the spacing. You need to get good overlap > in order to be able to do WHAM. If you don't know how to figure that out > then it's time for some reading. > > Good luck, > Chris. > > -- original message -- > > Hi Chris, > > Thank you very much for your detailed mail. > > Now I have a doubt on this pull_init parameter. i read your previous posts > regarding this, but still have a confusion. > > My query is that for each configuration when I run umbrella sampling, will > this pull_init value needs to change?(I suppose so, if its true how?) > > When it should be negative and positive? > > > Could you please explain this. Thanks for your valuable time > > Thanks & Regards, > Aswathy > > > On Mon, May 10, 2010 at 9:55 PM, Chris Neale >wrote: > > [Hide Quoted Text] > Pick a small collection of backbone atoms near the center of your channel > and use them as your reference group. Overcome the sign problem by optimal > selection of pull options (see below). pull_pbcatom values should not be > important > if you select your groups as I suggest -- otherwise be sure to understand > how they work. > > > ; COM PULLING > pull = umbrella > pull_geometry= position > pull_dim = N N Y > pull_start = no > pull_nstxout = 250 > pull_nstfout = 250 > pull_ngroups = 1 > pull_group0 = MY_SELECTION_OF_BACKBONE_ATOMS > pull_pbcatom0= 0 > pull_group1 = LIGAND > pull_pbcatom1= 0 > pull_init1 = 0 0 THISDIST > pull_rate1 = 0 > pull_k1 = 500.0 > pull_vec1= 0 0 0 > > Chris. > > -- original message -- > > I think Justin meant that you have various positions of the ligand in the > channel (from the SMD), so you don't need to make a new run to determine > new > positions in the channel. You need only new umbrella sampling simulations. > > Yep, the movement of the particle will also matter, because if the particle > moves much on the z-axis, the distance between the particle and the ligand > will change. So you would want the particle fixed relative to the channel. > Two ideas: > Place the particle above the entrance of the channel. Pick three atoms from > the entrance of the channel and determine the distance between the atoms > and > the particle. Then use distance_restraints or constraints with a > 'bondlength' equal to the measured distance. If everything goes right the > particle would stay where you placed it, since it does not interact with > the > enviroment it should not really influence your simulation (only through the > constraints or distance_restraints). > I don't now how big your system is, but it would probably be a good idea to > make a short test simulation, to look if the particle changes the system > behavior. > But it's only an idea, i hope other people comment it. > > Greetings > Thomas > > > -- > 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 thewww interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Aswathy -- 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] PMF of ligand transport
Hi, I tried to calculate PMF for the ligand transport using pull_geometry=position. Let me explain you what I did so far, I picked a small collection of backbone atoms nearly from the centre of the channel.My SMD was displacing the ligand from extracellular to intracellular. I checked the pullx file for getting the window spacing (pull_init ). Initial structure is at =7.61 Centre of the channel(reference) =8.20 Last displacement is at =8.91 Therfore I selected pul_init as 0.6, 0.5, 0.4 ,0-0.4,-0.5,-0.6 For example, the first frame(at 7.61) was sampled using the following parameters, pull = umbrella pull_geometry= position pull_dim = N N Y pull_start = no pull_nstxout = 10 pull_nstfout = 10 pull_ngroups = 1 pull_group0 = U_ref pull_pbcatom0= 0 pull_group1 = r_C1 pull_pbcatom1= 0pull_k1 = pull_init1 = 0 0 0.6 pull_k1 = 1000 pull_rate1 = 0 pull_vec1= 0 0 0 The problem is that the ligand undergoes a displacement to wrong direction during sampling. My idea was pull_k1 = 1000 is the force to keep ligand in one place where it get sampled? Is there anything wrong that I am doing? any suggestions will be appreciated. -Aswathy On Tue, May 11, 2010 at 11:15 AM, Aswathy wrote: > Hi Chris, > > Thank you very much for your detailed mail. > > Now I have a doubt on this pull_init parameter. i read your previous posts > regarding this, but still have a confusion. > > My query is that for each configuration when I run umbrella sampling, will > this pull_init value needs to change?(I suppose so, if its true how?) > > When it should be negative and positive? > > > Could you please explain this. Thanks for your valuable time > > Thanks & Regards, > Aswathy > > > > On Mon, May 10, 2010 at 9:55 PM, Chris Neale wrote: > >> Pick a small collection of backbone atoms near the center of your channel >> and use them as your reference group. Overcome the sign problem by optimal >> selection of pull options (see below). pull_pbcatom values should not be >> important >> if you select your groups as I suggest -- otherwise be sure to understand >> how they work. >> >> >> ; COM PULLING >> pull = umbrella >> pull_geometry= position >> pull_dim = N N Y >> pull_start = no >> pull_nstxout = 250 >> pull_nstfout = 250 >> pull_ngroups = 1 >> pull_group0 = MY_SELECTION_OF_BACKBONE_ATOMS >> pull_pbcatom0= 0 >> pull_group1 = LIGAND >> pull_pbcatom1= 0 >> pull_init1 = 0 0 THISDIST >> pull_rate1 = 0 >> pull_k1 = 500.0 >> pull_vec1= 0 0 0 >> >> Chris. >> >> -- original message -- >> >> I think Justin meant that you have various positions of the ligand in the >> channel (from the SMD), so you don't need to make a new run to determine new >> positions in the channel. You need only new umbrella sampling simulations. >> >> Yep, the movement of the particle will also matter, because if the >> particle moves much on the z-axis, the distance between the particle and the >> ligand will change. So you would want the particle fixed relative to the >> channel. >> Two ideas: >> Place the particle above the entrance of the channel. Pick three atoms >> from the entrance of the channel and determine the distance between the >> atoms and the particle. Then use distance_restraints or constraints with a >> 'bondlength' equal to the measured distance. If everything goes right the >> particle would stay where you placed it, since it does not interact with the >> enviroment it should not really influence your simulation (only through the >> constraints or distance_restraints). >> I don't now how big your system is, but it would probably be a good idea >> to make a short test simulation, to look if the particle changes the system >> behavior. >> But it's only an idea, i hope other people comment it. >> >> Greetings >> Thomas >> >> >> -- >> 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. Us
Re: [gmx-users] PMF of ligand transport
On Mon, May 17, 2010 at 12:14 PM, Aswathy wrote: > Hi, > > I tried to calculate PMF for the ligand transport using > pull_geometry=position. > > Let me explain you what I did so far, > > I picked a small collection of backbone atoms nearly from the centre of the > channel.My SMD was displacing the ligand from extracellular to > intracellular. > I checked the pullx file for getting the window spacing (pull_init ). > Initial structure is at =7.61 > Centre of the channel(reference) =8.20 > Last displacement is at =8.91 > > Therfore I selected pul_init as 0.6, 0.5, 0.4 ,0-0.4,-0.5,-0.6 > > For example, the first frame(at 7.61) was sampled using the following > parameters, > > pull = umbrella > pull_geometry= position > pull_dim = N N Y > pull_start = no > pull_nstxout = 10 > pull_nstfout = 10 > pull_ngroups = 1 > pull_group0 = U_ref > pull_pbcatom0= 0 > pull_group1 = r_C1 > pull_pbcatom1= 0 > pull_init1 = 0 0 0.6 > pull_k1 = 1000 > pull_rate1 = 0 > > pull_vec1= 0 0 0 > > The problem is that the ligand undergoes a displacement to wrong direction > during sampling. My idea was pull_k1 = 1000 is the force to keep ligand in > one place where it get sampled? > I want to add some more points to this. I agree that as I am using the "Position" , it should be displaced to the position of reference. But my worry is that, when i visualize this trajectory, within the first two or three frames, ligand get displaced. As per my u understanding, we need to sample well at the same position to get the PMF at that point.(Is it so?) in that case, the sudden drop from the initial position will cause any problem in the PMF? > Is there anything wrong that I am doing? > any suggestions will be appreciated. > > -Aswathy > > > > On Tue, May 11, 2010 at 11:15 AM, Aswathy wrote: > >> Hi Chris, >> >> Thank you very much for your detailed mail. >> >> Now I have a doubt on this pull_init parameter. i read your previous >> posts regarding this, but still have a confusion. >> >> My query is that for each configuration when I run umbrella sampling, will >> this pull_init value needs to change?(I suppose so, if its true how?) >> >> When it should be negative and positive? >> >> >> Could you please explain this. Thanks for your valuable time >> >> Thanks & Regards, >> Aswathy >> >> >> >> On Mon, May 10, 2010 at 9:55 PM, Chris Neale wrote: >> >>> Pick a small collection of backbone atoms near the center of your channel >>> and use them as your reference group. Overcome the sign problem by optimal >>> selection of pull options (see below). pull_pbcatom values should not be >>> important >>> if you select your groups as I suggest -- otherwise be sure to understand >>> how they work. >>> >>> >>> ; COM PULLING >>> pull = umbrella >>> pull_geometry= position >>> pull_dim = N N Y >>> pull_start = no >>> pull_nstxout = 250 >>> pull_nstfout = 250 >>> pull_ngroups = 1 >>> pull_group0 = MY_SELECTION_OF_BACKBONE_ATOMS >>> pull_pbcatom0= 0 >>> pull_group1 = LIGAND >>> pull_pbcatom1= 0 >>> pull_init1 = 0 0 THISDIST >>> pull_rate1 = 0 >>> pull_k1 = 500.0 >>> pull_vec1= 0 0 0 >>> >>> Chris. >>> >>> -- original message -- >>> >>> I think Justin meant that you have various positions of the ligand in the >>> channel (from the SMD), so you don't need to make a new run to determine new >>> positions in the channel. You need only new umbrella sampling simulations. >>> >>> Yep, the movement of the particle will also matter, because if the >>> particle moves much on the z-axis, the distance between the particle and the >>> ligand will change. So you would want the particle fixed relative to the >>> channel. >>> Two ideas: >>> Place the particle above the entrance of the channel. Pick three atoms >>> from the entrance of the channel and determine the distance between the >>> atoms and the parti
[gmx-users] Fwd: reproducibility of PMF plot with two different starting structures?
Hi, I just want to know about the consistency we could obtain in plotting PMF. I am using Gromacs 4.0.4 MPI version. Trying to find the PMF of the ligand transport through the channel. I tried two SMDs (same pull rate, and force constant) with different starting structures (only ligand poses and position are slightly different). I performed the sampling of these two pathways, the plots obtained are of similar overall shapes, but peaks (max , min) have some variations? Could you please give your comment on this attempt? Is that expectable? Thank you, -- Aswathy -- Aswathy -- 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] Enough hydration of the channel
Hi everyone, I have a homology model of a transporter. I want to study the ligand transport through the channel. i have done the following steps. 1. Ligand has docked to the mouth of the channel 2. Inserted the complex in POPC bilayer, then solvated, and equilibrated for 4ns(with position restarint on Protein & ligand) 3. Then I saw tht there are very few wtaer inside the pore, Since this channel is an aqueous pore, I have added water to the channel using genbox. 4. Then the complete system equilibrated for pico seconds. 5,in order to select different snap shots for SMD (want to do a multiple SMDs with different starting structures.) I have run 1ns Production run and selected different frames. Suddenly I found that still there is no enough water in the pore, the water is moving away from the channel during step 4 &5? How can I solve this problem? Also how will I know how many water molecules will be sufficient for the channel? Thanks for your support. -- Aswathy -- 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] Enough hydration of the channel
Thank you very much. In some papers I have seen the graph for hydration of the channel. How can we calculate that using Gromacs ? (or any other program?) Regards, -Aswathy On Thu, Jun 17, 2010 at 7:52 PM, wrote: > Determining how many waters is sufficient is a tough problem, try > successive runs of option #3, below. As for the simpler topic of getting > more hydration: > > 1. If the issue is simply getting the channel hydrated enough to overcome > some transition from dry to wet, then run a neat water box od 216 spc for > 100 ps and extract a frame every 10 ps, then run genbox 10x successively > using each of these frames. This should give you massive hydration. > > 2. If that doesn't work, then you could add a new equilibration step where > you posres some cap waters so that the channel can not dry out. This may > allow SC's to equilibrate to a wet environment. > > 3. If the issue is that the water is still moving out, then why not do SMD > on a water into the pore and find out where the repulsion is. > > -- original message -- > > Hi everyone, > > I have a homology model of a transporter. I want to study the ligand > transport through the channel. i have done the following steps. > > 1. Ligand has docked to the mouth of the channel > 2. Inserted the complex in POPC bilayer, then solvated, and equilibrated > for 4ns(with position restarint on Protein & ligand) > 3. Then I saw tht there are very few wtaer inside the pore, Since this > channel is an aqueous pore, I have added water to the channel using genbox. > 4. Then the complete system equilibrated for pico seconds. > 5,in order to select different snap shots for SMD (want to do a multiple > SMDs with different starting structures.) I have run 1ns Production run and > selected different frames. > > Suddenly I found that still there is no enough water in the pore, the water > is moving away from the channel during step 4 &5? > > How can I solve this problem? Also how will I know how many water molecules > will be sufficient for the channel? > > Thanks for your support. > > > -- > 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 thewww interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Aswathy -- 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] Enough hydration of the channel
Thanks a lot. On Fri, Jun 18, 2010 at 9:30 AM, Justin A. Lemkul wrote: > > > Aswathy wrote: > >> Thank you very much. >> >> In some papers I have seen the graph for hydration of the channel. How can >> we calculate that using Gromacs ? (or any other program?) >> > > Have a look at some of Oliver Beckstein's programs: > > http://sbcb.bioch.ox.ac.uk/oliver/software/ > > There are several that might be useful to you. > > -Justin > > >> Regards, >> -Aswathy >> >> >> >> On Thu, Jun 17, 2010 at 7:52 PM, > chris.ne...@utoronto.ca>> wrote: >> >>Determining how many waters is sufficient is a tough problem, try >>successive runs of option #3, below. As for the simpler topic of >>getting more hydration: >> >>1. If the issue is simply getting the channel hydrated enough to >>overcome some transition from dry to wet, then run a neat water box >>od 216 spc for 100 ps and extract a frame every 10 ps, then run >>genbox 10x successively using each of these frames. This should give >>you massive hydration. >> >>2. If that doesn't work, then you could add a new equilibration step >>where you posres some cap waters so that the channel can not dry >>out. This may allow SC's to equilibrate to a wet environment. >> >>3. If the issue is that the water is still moving out, then why not >>do SMD on a water into the pore and find out where the repulsion is. >> >>-- original message -- >> >>Hi everyone, >> >>I have a homology model of a transporter. I want to study the ligand >>transport through the channel. i have done the following steps. >> >>1. Ligand has docked to the mouth of the channel >>2. Inserted the complex in POPC bilayer, then solvated, and >>equilibrated >>for 4ns(with position restarint on Protein & ligand) >>3. Then I saw tht there are very few wtaer inside the pore, Since this >>channel is an aqueous pore, I have added water to the channel using >>genbox. >>4. Then the complete system equilibrated for pico seconds. >>5,in order to select different snap shots for SMD (want to do a >> multiple >>SMDs with different starting structures.) I have run 1ns Production >>run and >>selected different frames. >> >>Suddenly I found that still there is no enough water in the pore, >>the water >>is moving away from the channel during step 4 &5? >> >>How can I solve this problem? Also how will I know how many water >>molecules >>will be sufficient for the channel? >> >>Thanks for your support. >> >> >>-- gmx-users mailing listgmx-users@gromacs.org >> <mailto:gmx-users@gromacs.org> >> >>http://lists.gromacs.org/mailman/listinfo/gmx-users >>Please search the archive at http://www.gromacs.org/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 >><mailto:gmx-users-requ...@gromacs.org>. >> >>Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> >> >> >> >> -- >> Aswathy >> >> > -- > > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/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 > -- Aswathy -- 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] Query on WHAM analysis
Hi all, I am doing the umbrella sampling of a ligand pathway (Gromacs4.0.4).Now i want to plot the PMF using WHAM analysis by Alan Grossfield. I installed the WHAM program, read the manual too. But i am confused with the "loc_win_min" and "spring" terms in the metadata file. Can anyone please explain me these two terms? I have the pullx files from 21 umbrella samplings.(I guess this will go as the first term in the meta data file.). Pull_k1 used for Us was 1000. Please let me know if you need any other details. Thanks in advance, -Aswathy -- 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] umbrella sampling-Bimodal Histograms
Hi Friends, When i did the Umbrella sampling of frames from an SMD (of ligand transport), I am getting bimodal histograms in some cases. Do you think this is because , the force constant that i used is very low (i used pull_k1=1000).? Are these bimodal peaks may cause any deviation in my PMF result? Do I need to repeat the sampling again with another pull_k1 value(higher value)? Thanks, -- Aswathy -- Aswathy -- 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] umbrella sampling-Bimodal Histograms
I am doing US . Yes, histograms of population densities along the reaction coordinate. Please find the pull settings. Sampled for 800ps.(nsteps = 40). Pull_init will vary for each frame, depends on the window spacing. pull = umbrella pull_geometry= position pull_dim = N N Y pull_start = no pull_nstxout = 10 pull_nstfout = 10 pull_ngroups = 1 pull_group0 = U_ref pull_pbcatom0= 0 pull_group1 = r_C1 pull_pbcatom1= 0 pull_init1 = 0 0 0.1 pull_k1 = 1000 pull_rate1 = 0 pull_vec1= 0 0 0 Please check this link for my histograms https://docs.google.com/fileview?id=0B1PyTWWGrqt6MDU3NWYwMGUtNjY5Zi00NDBmLWE0YzMtYTNjODVlOGFlNWVl&hl=en I would greatly appreciate our suggestions. Thank you, -Aswathy On Mon, Jun 21, 2010 at 8:14 PM, wrote: > Please clarify: > > Are doing SMD or are you doing US? If you're doing SMD then you should not > be using WHAM and you should not really be able to generate any sampling > histograms. > > Are the histograms that you are referring to population densities of the > sampling along your reaction coordinate? > > My guess -- if you're doing US -- is that you have some incorrect pull > group settings. Bimodal distributions are indeed possible, but should > require very long sampling times to achieve, and I doubt that you are at > those times yet. Your Fc is fine. Post your pull settings. > > Chris. > > -- original message -- > > When i did the Umbrella sampling of frames from an SMD (of ligand > transport), I am getting bimodal histograms in some cases. > > Do you think this is because , the force constant that i used is very low > (i > used pull_k1=1000).? Are these bimodal peaks may cause any deviation in my > PMF result? Do I need to repeat the sampling again with another pull_k1 > value(higher value)? > > > > -- > 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 thewww interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Aswathy -- 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] umbrella sampling-Bimodal Histograms
I took initial 300 as equilibration,Now it seems fine. Thank you .. On Tue, Jun 22, 2010 at 9:21 AM, wrote: > Take that replica on the left that shows a bimodal histogram. Now plot a > time series of the displacement: x-axis = time and y-axis = displacement > along reaction coord. Is it jumping back and forth between two regions of > sampling? Probably not... more likely it starts near one maximum and > transitions to another maximum. > > If this is true then it simply means that you have not equilibrated enough. > Run longer and cut some of the initial sampling. > > Chris. > > -- original message -- > > I am doing US . Yes, histograms of population densities along the reaction > coordinate. Please find the pull settings. Sampled for 800ps.(nsteps = > 40). Pull_init will vary for each frame, depends on the window spacing. > > pull = umbrella > pull_geometry= position > pull_dim = N N Y > pull_start = no > pull_nstxout = 10 > pull_nstfout = 10 > pull_ngroups = 1 > pull_group0 = U_ref > pull_pbcatom0= 0 > pull_group1 = r_C1 > pull_pbcatom1= 0 > pull_init1 = 0 0 0.1 > pull_k1 = 1000 > pull_rate1 = 0 > pull_vec1= 0 0 0 > > Please check this link for my histograms > > > https://docs.google.com/fileview?id=0B1PyTWWGrqt6MDU3NWYwMGUtNjY5Zi00NDBmLWE0YzMtYTNjODVlOGFlNWVl&hl=en > > I would greatly appreciate our suggestions. > > Thank you, > -Aswathy > > On Mon, Jun 21, 2010 at 8:14 PM, wrote: > > Please clarify: >> >> Are doing SMD or are you doing US? If you're doing SMD then you should not >> be using WHAM and you should not really be able to generate any sampling >> histograms. >> >> Are the histograms that you are referring to population densities of the >> sampling along your reaction coordinate? >> >> My guess -- if you're doing US -- is that you have some incorrect pull >> group settings. Bimodal distributions are indeed possible, but should >> require very long sampling times to achieve, and I doubt that you are at >> those times yet. Your Fc is fine. Post your pull settings. >> >> Chris. >> >> -- original message -- >> >> When i did the Umbrella sampling of frames from an SMD (of ligand >> transport), I am getting bimodal histograms in some cases. >> >> Do you think this is because , the force constant that i used is very low >> (i >> used pull_k1=1000).? Are these bimodal peaks may cause any deviation in my >> PMF result? Do I need to repeat the sampling again with another pull_k1 >> value(higher value)? >> > > > -- > 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 thewww interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Aswathy -- 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] Pullx file
Dear friends, I have pulled a ligand through the channel. Here i kept one residue at the mouth of the channel as reference and group1 is one of the atom in the side chain of the ligand. Now I have the pullx file,( and here 1dz is the z coordinate of group1-group0), but here I would like to have z-coordiante of the ligand(instead of the single atom at the side chain)-group1. Becuase I beleive , that will give the correct position of the ligand (please correct me if I am wrong) Is there any way to do this without running the SMD again? I have plotted the g_dist between the reference group and the ligand. But that does not take the place of pullx. Please give your suggestions. Thanks, -- Aswathy -- 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] Problem in pullx file
Dear Gromacs users, I am doing SMD of a ligand pathway, and then want ot do the PMF analysis. Initially I pulled the ligand from extra to intracellular side of the protein. The pull code used are given below. pull = umbrella pull_geometry= distance pull_dim = N N Y pull_start = yes pull_nstxout = 10 pull_nstfout = 10 pull_ngroups = 1 pull_group0 = r_57 pull_group1 = r_C1 pull_rate1 = 0.005 pull_k1 = 1000 here group0 is one residue at the extracellular region and r_C1 is the side chain Carbon atom of the ligand. My question is , the total length of the channel is almost 40 Angstrom and as per my knowledge, when we did the pulling the pullx file will give the coordinate of the ligand through the channel. Even though ligand reaches the opposite end of the channel, in pullx file I am getting around 19 Angstrom in total. Again I calculate the g_dist of the ligand and the center of the channel, it shows around 40 Ang in total . Please find the links provided Am I misunderstanding anything about the pullx file. Could you please suggest me where thing get wrong? http://docs.google.com/fileview?id=0B1PyTWWGrqt6N2IyNjNhM2UtMzRiZC00MTJmLTg5ODItODJlMzQ5YTM3OGMy&hl=en http://docs.google.com/fileview?id=0B1PyTWWGrqt6ZWRlZGJkOTgtMGEwYi00MzE0LThiZTEtM2JjNmJkMWU5NDYy&hl=en Thank you, -- -Aswathy -- 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] Problem in pullx file
On Wed, Aug 4, 2010 at 4:31 PM, Justin A. Lemkul wrote: > > > Aswathy wrote: > >> Dear Gromacs users, >> >> I am doing SMD of a ligand pathway, and then want ot do the PMF analysis. >> Initially I pulled the ligand from extra to intracellular side of the >> protein. The pull code used are given below. >> >> pull = umbrella >> pull_geometry= distance >> pull_dim = N N Y >> pull_start = yes >> pull_nstxout = 10 >> pull_nstfout = 10 >> pull_ngroups = 1 >> pull_group0 = r_57 >> pull_group1 = r_C1 >> pull_rate1 = 0.005 >> pull_k1 = 1000 >> >> here group0 is one residue at the extracellular region and r_C1 is the >> side chain Carbon atom of the ligand. >> >> My question is , the total length of the channel is almost 40 Angstrom and >> as per my knowledge, when we did the pulling the pullx file will give the >> coordinate of the ligand through the channel. >> > > Not quite. Look at the data labels in the .xvg file. The pullx file > contains the coordinates (in all of the pull directions) for the reference > group, and then the distance between the reference and the pull group along > all pull axes. I am still confused. I have measured the distance between the reference group(residue outside) to the other end of the channel. that is around 40Angstrom. if so, 1dz should give around 40 Angstrom? Because once the pulling completed, the distance between group0 and group1 , should be equal to the length of the channel. Sorry that i am repeating the same query, i think I am still preconceived about this. Otherwise could you please suggest some good tutorial for the same . I will read that. > > Even though ligand reaches the opposite end of the channel, in pullx file >> I am getting around 19 Angstrom in total. >> >> Again I calculate the g_dist of the ligand and the center of the channel, >> it shows around 40 Ang in total . Please find the links provided >> >> > You're measuring two different things. The pullx distance is given > relative to your pull_group0, which you said is a residue on one side of the > channel. Then you're using g_dist to measure to the center of the channel. > > Am I misunderstanding anything about the pullx file. >> >> Could you please suggest me where thing get wrong? >> >> >> http://docs.google.com/fileview?id=0B1PyTWWGrqt6N2IyNjNhM2UtMzRiZC00MTJmLTg5ODItODJlMzQ5YTM3OGMy&hl=en< >> http://docs.google.com/fileview?id=0B1PyTWWGrqt6N2IyNjNhM2UtMzRiZC00MTJmLTg5ODItODJlMzQ5YTM3OGMy&hl=en >> > >> >> >> http://docs.google.com/fileview?id=0B1PyTWWGrqt6ZWRlZGJkOTgtMGEwYi00MzE0LThiZTEtM2JjNmJkMWU5NDYy&hl=en< >> http://docs.google.com/fileview?id=0B1PyTWWGrqt6ZWRlZGJkOTgtMGEwYi00MzE0LThiZTEtM2JjNmJkMWU5NDYy&hl=en >> > >> >> > For some reason these documents are inaccessible. It is probably better to > use a site like photobucket and post actual images. Google is great, but > not everyone has an account and I've also been told that their usage > agreement is troubling, in that anything you upload to Google Docs becomes > property of Google. Not something I've looked into, but I don't ever post > my research data there. > > > -Justin > > >> Thank you, >> -- >> -Aswathy >> >> > -- > > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/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 > -- Aswathy -- 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] Problem in pullx file
Let me explain. Consider the channel of a membrane protein, r57 is a residue at the extracellular loop in this channel. I docked my ligand to the start of the channel. ie; just below the r57. (Here the I have not started from the solvent, but at the mouth of the channel , just below r 57..) Then I pulled the ligand through the channel(parameters as in the first mail). ie; pulled in such a way that, initially ligand was just below r57, then moved away from r57. Plz check some data from the pullx file. 0.7.74891-0.754818 0.02007.74388-0.754379 0.04007.73726-0.752573 0.06007.73032-0.756692 0.08007.72422-0.747781 0.10007.72041-0.754858 0.12007.71691-0.744501 .. .. .. 1099.86018.455715.46432 1099.88008.45551-5.46076 1099.90008.45817-5.46827 1099.92008.460755.46829 1099.94018.46317-5.46782 1099.96018.465455.46577 1099.98018.46565-5.47014 1100.8.466515.46001 Thanks, Aswathy On Thu, Aug 5, 2010 at 4:28 PM, Justin A. Lemkul wrote: > > > Aswathy wrote: > > >> >> On Wed, Aug 4, 2010 at 4:31 PM, Justin A. Lemkul > jalem...@vt.edu>> wrote: >> >> >> >>Aswathy wrote: >> >>Dear Gromacs users, >> >>I am doing SMD of a ligand pathway, and then want ot do the PMF >>analysis. Initially I pulled the ligand from extra to >>intracellular side of the protein. The pull code used are given >>below. >> >>pull = umbrella >>pull_geometry= distance >>pull_dim = N N Y >>pull_start = yes >>pull_nstxout = 10 >>pull_nstfout = 10 >>pull_ngroups = 1 >>pull_group0 = r_57 >>pull_group1 = r_C1 >>pull_rate1 = 0.005 >>pull_k1 = 1000 >> >>here group0 is one residue at the extracellular region and r_C1 >>is the side chain Carbon atom of the ligand. >> >>My question is , the total length of the channel is almost 40 >>Angstrom and as per my knowledge, when we did the pulling the >>pullx file will give the coordinate of the ligand through the >>channel. >> >> >>Not quite. Look at the data labels in the .xvg file. The pullx >>file contains the coordinates (in all of the pull directions) for >>the reference group, and then the distance between the reference and >>the pull group along all pull axes. >> >> I am still confused. I have measured the distance between the reference >> group(residue outside) to the other end of the channel. that is around >> 40Angstrom. if so, 1dz should give around 40 Angstrom? Because once the >> pulling completed, the distance between group0 and group1 , should be equal >> to the length of the channel. >> >> > I guess I still don't understand your setup. Are you pulling a ligand > through a a channel and then beyond the reference group, out into some > solvent? Or are you just pulling the length of the channel, such that the > ligand never exits the channel. > > If you're pulling through the entire channel and then out into the solvent, > the sign of dZ is going to change. It might help if you post the first few > output lines of pullx.xvg (not the headers and stuff, the actual data), as > well as the last few. That way I can understand exactly what you're dealing > with. > > > Sorry that i am repeating the same query, i think I am still preconceived >> about this. Otherwise could you please suggest some good tutorial for the >> same . I will read that. >> >> > There is a pulling tutorial on the Gromacs website, but nothing that deals > with what you're doing. Tutorials are designed to generally guide the user > through a larger procedure, not explain every small piece of analysis. > > -Justin > > >> >> >>Even though ligand reaches the opposite end of the channel, in >>pullx file I am getting around 19 Angstrom in total. >> >>Again I calculate the g_dist of the ligand and the center of the >>channel, it shows around 40 Ang in total . Please find the links >>provided >> >> >>You're measuring two different things. The pullx
[gmx-users] Electrostatic interaction Vs Z axis
Dear Gromacs users, I want to find the electrostatic interaction energy between ligand and protein, water and ligand during SMD of the ligand through the channel. I have used g_energy but, I need to plot the energy against Z axis of the channel. Could you please help me. Thanks in advance, -- Aswathy -- 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] Umbrella sampling question
Hi Gromacs users, Let me give an idea about what i am doing. I was doing a Steered Molecular dynamics of ligand transport through the transporter channel. I want to do the PMF calculation using Umbrella sampling. I followed the steps provided in the (Justin's) tutorial. I have generated all configurations, then used the perl script to find out the distance. I made one index group for 3 back bone atoms at the center of the channel and another for the ligand. (Therefore I will get the distance between the center of the channel and ligand). Then I sampled each frame with a window spacing of 0.1nm. The frame close to the center of the channel is taken at the 0 th coordinate(pull_init=0 0 0). above this point is +Z coordinate and below this point is -Z coordinate. I had good overlapped histograms and went ahead with plotting PMF. Am I doing the correct procedure for Umbrella sampling? Why I doubt because, I run g_wham and I had a PMF plot in which at the starting of the transport (from extracellular), I have free energy value of -35kcal/mol. Then as it moves along the pathway it increases and finally it reaches a positive value, +5kcal (when at intracellular). I know its hard give explanation to my observation, but I am confused due to several reasons. 1.The energy increases is not much explainable with interactions of ligand and transporter. 2.If I take the free energy barrier value it is great value than I expected. Nearly 170KJ/mol 3.In similar kind of ligand transport Smds the PMF was continuous maxima and minima. Can any one tell whether my US procedures were right or not? Thanks, -- Aswathy -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Umbrella sampling question
Hi Chris, Thank you very much for your reply. I will give you more details on my US. Initially ligand is positioned at the starting of the channel and pulled down wards.(SMD) 1. I have generated all configurations from the SMD(trjconv). 2. Created one index group for center of the channel and another for ligand. 3. Generated a summary_distance file (g_dist) using these index groups 4. Window spacing selected as 0.1nm. 5. run Us with the follo: p[arameters. pull = umbrella pull_geometry= position pull_dim = N N Y pull_start = no pull_nstxout = 10 pull_nstfout = 10 pull_ngroups = 1 pull_group0 = U_ref(channel center) pull_pbcatom0= 0 pull_group1 = LIG pull_pbcatom1= 0 pull_init1 = 0 0 0 pull_k1 = 1000 pull_rate1 = 0 pull_vec1= 0 0 0 pull_init 0 0 0 represent the sampling of minimum g_dist value (ligand near to center of the channel). for positive Z axis, it may change as 0 0 0.1, 0, 0, 0.2 etc. along -z axis, it is 0 0 -0.1, 0, 0, -0.2 etc. 6. initial 400PS took as equilibration during PMF plot. http://s980.photobucket.com/albums/ae290/aswathys/?action=view¤t=PROFILE-eq400.jpg If the PMf is not converged, does it means we need to sample more time or with higher force constant or need to sample more configurations? Could you please tell me more on the point that you suggested "check the probability histograms and ensuring that they tend away from the center of restraint and toward local minima". ? Thanks in advance. On Mon, Sep 20, 2010 at 6:22 PM, wrote: > Aswathy: > > We can't tell if you did US correctly unless you post what you have done. > You must give more info and you must copy and paste the actual input / .mdp > parameters that you used. > > As for if your PMF is correct, then we can never tell you that. You can, > however, ensure that your sampling distributions are compatible with the PMF > that you get out of WHAM by looking at the probability histograms and > ensuring that they tend away from the center of restraint and toward local > minima on your PMF. > > There are hundreds of reasons why your PMF might be wrong (note that it > also might be correct!) but that is impossible for us to tell with the > information that you have provided. At the very least, one would need to see > the PMF and all of the info I mentioned above. Also, you should check (and > show us!) convergence. If you PMF is still drifting with increasing sampling > (or increased initial time discarded as equilibration) then you are simply > not converged for sure. > > Chris. > > -- original message -- > > Hi Gromacs users, > Let me give an idea about what i am doing. > I was doing a Steered Molecular dynamics of ligand transport through > the transporter channel. I want to do the PMF calculation using > Umbrella sampling. I followed the steps provided in the (Justin's) > tutorial. I have generated all configurations, then used the perl > script to find out the distance. I made one index group for 3 back > bone atoms at the center of the channel and another for the ligand. > (Therefore I will get the distance between the center of the channel > and ligand). > Then I sampled each frame with a window spacing of 0.1nm. The frame > close to the center of the channel is taken at the 0 th > coordinate(pull_init=0 0 0). above this point is +Z coordinate and > below this point is -Z coordinate. I had good overlapped histograms > and went ahead with plotting PMF. > > Am I doing the correct procedure for Umbrella sampling? > Why I doubt because, > I run g_wham and I had a PMF plot in which at the starting of the > transport (from extracellular), I have free energy value of > -35kcal/mol. Then as it moves along the pathway it increases and > finally it reaches a positive value, +5kcal (when at intracellular). > > I know its hard give explanation to my observation, but I am confused > due to several reasons. > 1.The energy increases is not much explainable with interactions of > ligand and transporter. > 2.If I take the free energy barrier value it is great value than I > expected. Nearly 170KJ/mol > 3.In similar kind of ligand transport Smds the PMF was continuous > maxima and minima. > > Can any one tell whether my US procedures were right or not? > > Thanks, > > > -- > Aswathy > > > -- > 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 thewww interface > or sen
[gmx-users] How can I create the OPLS-AA topology file for the liagnd
Hi, i would like to do a ligand -receptor simulation using OPLS-AA force field. I suppose using the options in Gromacs I can create the itp files for protein only. But how can i create the OPLS --AA topology file for the ligand. I think PRODRG server only creates gromacs force field. Please coreect me if my understanding is wrong. Thanks in advance, Aswathy ___ 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] ERROR: pressure coupling not enough values (I need 1)
Hi, thanks for the help till now.. Now I got a problem that an equilibration step of 20 ps shows an error as follows when i run grommp. ERROR: pressure coupling not enough values (I need 1) Please find the md.mdp file that I have used for this step. thanks, Aswathy Dept. Biotechnology Ext. 3108 md.mdp 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] ERROR: pressure coupling not enough values (I need 1)
I have specified ref_p as 1, now grommp works fine.but show the error as below. From the previous post what I understood is this is a problem with the gromacs version. I am using Gromacs3.2.1. Is that could be the problem?? Back Off! I just backed up minim+ener.edr to ./#minim+ener.edr.2# starting mdrun 'Protein in water' 1 steps, 20.0 ps. Back Off! I just backed up RBP4_em_eq1_20ps.trr to ./#RBP4_em_eq1_20ps.trr.2# Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: max 1428.842651 (between atoms 1547 and 1548) rms 43.118099 bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 50 51 93.10.1530 1.1319 0.1530 51 52 92.80.1470 4.0768 0.1470 52 53 95.00.1000 3.3258 0.1000 52 54 93.70.1340 9.4062 0.1340 54 55 93.20.1340 8.3665 0.1340 54 58 90.50.1340 47.1335 0.1340 55 56 91.60.1000 4.4466 0.1000 55 57 91.50.1000 4.4648 0.1000 58 59 90.20.1000 48.3157 0.1000 58 60 90.20.1000 47.7912 0.1000 74 75 90.00.1430 0.9637 0.1430 75 76 90.00.1000 0.3743 0.1000 112116 30.30.1340 0.1354 0.1340 116117 36.70.1000 0.1036 0.1000 116118 52.90.1000 0.1068 0.1000 156158 88.60.1330 0.1471 0.1330 158159 89.50.1000 0.1658 0.1000 158160 89.40.1000 0.1357 0.1000 314315 90.00.1780 0.3872 0.1780 474475 94.70.1530 0.0262 0.1530 475476 91.50.1530 0.3873 0.1530 476477 90.50.1250 0.7752 0.1250 476478 91.90.1250 0.3319 0.1250 677678 93.20.1530 0.3123 0.1530 678679 92.80.1530 0.9707 0.1530 679680 92.40.1230 0.9836 0.1230 679681 90.60.1330 3.5962 0.1330 681682 90.20.1000 3.8687 0.1000 681683 90.20.1000 3.6579 0.1000 1200 1204 36.10.1390 0.1420 0.1390 1204 1205 90.00.1080 1.8158 0.1080 1204 1206 33.90.1390 0.1433 0.1390 1542 1544 98.50.1470 0.6632 0.1470 1544 1545 94.30.1530 5.8372 0.1530 1544 1552 98.50.1530 0.6695 0.1530 1545 1546 91.30.1530 39.3403 0.1530 1546 1547 93.30.1530 69.5871 0.1530 1547 1548 91.10.1230 175.8707 0.1230 1547 1549 93.20.1330 71.3069 0.1330 1549 1550 91.50.1000 39.8680 0.1000 1549 1551 91.40.1000 40.0342 0.1000 1625 1626 38.00.1000 0.1028 0.1000 1625 1627 32.70.1000 0.1012 0.1000 1715 1717 39.90.1330 0.1337 0.1330 1717 1718 64.00.1000 0.1027 0.1000 1717 1719 63.00.1000 0.1019 0.1000 Back Off! I just backed up step-1.pdb to ./#step-1.pdb.2# Back Off! I just backed up step0.pdb to ./#step0.pdb.2# Wrote pdb files with previous and current coordinates step 0 MPI process rank 0 (n0, p9393) caught a SIGSEGV. Thanks, Aswathy Dept. Biotechnology Ext. 3108 - Original Message - From: "Justin A. Lemkul" To: "Discussion list for GROMACS users" Sent: Friday, June 12, 2009 4:31:28 PM GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi Subject: Re: [gmx-users] ERROR: pressure coupling not enough values (I need 1) Ms. Aswathy S wrote: > Hi, > > thanks for the help till now.. > > Now I got a problem that an equilibration step of 20 ps shows an error as > follows when i run grommp. > > ERROR: pressure coupling not enough values (I need 1) > > Please find the md.mdp file that I have used for this step. > You haven't specified ref_p. -Justin > > thanks, > Aswathy > Dept. Biotechnology > Ext. 3108 > > > > > ___ > 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] Error in hdb file ffG43a1.hdb
Hi, I have upgraded my gromacs version to 3.3.3 from 3.2.1. When I tried to run the pdb2gmx i got the follo: error. From the previous post I guess that i should edit this ffG43a1.hdb. but my input is a protein file so ..so is this necessary or any other way to rectify this problem??? --- Program pdb2gmx_mpi, VERSION 3.3.3 Source code file: h_db.c, line: 95 Fatal error: Error in hdb file ffG43a1.hdb: Wrong number of control atoms (2 iso 3) on line: 1 1 N -C CA Thanks in advance, Aswathy Dept. Biotechnology Ext. 3108 ___ 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] Error in hdb file ffG43a1.hdb
Please ignore this post. I rectified the problem by using the GMXLIB export. Thank you very much for all the support Aswathy Dept. Biotechnology Ext. 3108 - Original Message - From: "Ms. Aswathy S" To: "gmx-users" Sent: Saturday, June 13, 2009 12:00:11 PM GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi Subject: [gmx-users] Error in hdb file ffG43a1.hdb Hi, I have upgraded my gromacs version to 3.3.3 from 3.2.1. When I tried to run the pdb2gmx i got the follo: error. From the previous post I guess that i should edit this ffG43a1.hdb. but my input is a protein file so ..so is this necessary or any other way to rectify this problem??? --- Program pdb2gmx_mpi, VERSION 3.3.3 Source code file: h_db.c, line: 95 Fatal error: Error in hdb file ffG43a1.hdb: Wrong number of control atoms (2 iso 3) on line: 1 1 N -C CA Thanks in advance, Aswathy Dept. Biotechnology Ext. 3108 ___ 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 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] problem in ngmx
Hi, after equlibration of my protein and ligand I tried to create the energy file ans well as the to display the trajectories using ngmx option,. But it shows the follo: error, Xlib: connection to ":0.0" refused by server Xlib: No protocol specified Can't connect to X Server. Check your DISPLAY environment variable also the g_energy command shows that , Program g_energy_mpi, VERSION 3.3.3 Source code file: enxio.c, line: 239 Fatal error: Energy file eq_2ps_ener.edr not recognized, maybe different CPU? Can any one help me, please??? Thanks, Aswathy ASBT Dept. Biotechnology Ext. 3108 ___ 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] problem in ngmx
Thank you very much for the reply... gmxcheck of my out shows a "segementation fault" in the last part. What could be the problem?? this is the last part of the output x[31416] (-7.37978e-03 6.79718e+00 6.07531e+00) - (-7.4e-03 6.79720e+00 6.07530e+00) x[31428] ( 2.35365e-01 -6.53947e-03 5.65519e+00) - ( 2.35400e-01 -6.5e-03 5.65520e+00) x[31478] ( 1.54478e-02 6.14019e+00 5.74537e+00) - ( 1.54000e-02 6.14020e+00 5.74540e+00) Segmentation fault The energy minimisation & the equilibration steps are finished at 15 step eventhough it was given for 20 ps(1 steps).But the output coordinates file doesnt show any abnornmality as i checked in the viewer? My equilibration step was in NVT. whether nothing is happening or any other problem? Thanks & regards, Aswathy Dept. Biotechnology Ext. 3108 - Original Message - From: "Manik Mayur" To: "Discussion list for GROMACS users" , jalem...@vt.edu Sent: Saturday, June 13, 2009 5:34:08 PM GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi Subject: Re: [gmx-users] problem in ngmx On Sat, Jun 13, 2009 at 5:14 PM, Florian Dommert < domm...@icp.uni-stuttgart.de > wrote: * Justin A. Lemkul < jalem...@vt.edu > [2009-06-13 07:31:17 -0400]: Ms. Aswathy S wrote: Hi, after equlibration of my protein and ligand I tried to create the energy file ans well as the to display the trajectories using ngmx option,. But it shows the follo: error, Xlib: connection to ":0.0" refused by server Xlib: No protocol specified Can't connect to X Server. Check your DISPLAY environment variable Seems like your X environment is somehow not properly configured. If you are working through ssh, then you can : $export DISPLAY=:0.0 Or you are tunneling through a SSH connection. There are several possiblities: 1. Try ssh -X to login, this could solve the problem, if you are in principle allowed to use X11 tunneling. 2. In case this does not work either it can be that you are not allowed to tunnel X11. However take care that you also need a properly configured XServer running on your own system not just on the host you login. So in case you use Windows or MacOS make sure this is the case. Flo also the g_energy command shows that , Program g_energy_mpi, VERSION 3.3.3 Source code file: enxio.c, line: 239 Fatal error: Energy file eq_2ps_ener.edr not recognized, maybe different CPU? What does gmxcheck tell you about the file. Perhaps it has been corrupted in some way. Also, you may want to work with a more current version (4.0.5) to utilize the newest features and bug fixes. -Justin Can any one help me, please??? Thanks, Aswathy ASBT Dept. Biotechnology Ext. 3108 ___ 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 -- Florian Dommert Dipl.-Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart Tel: +49 - 711 / 6856-3613 Fax: +49 - 711 / 6856-3658 EMail: domm...@icp.uni-stuttgart.de Home: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert !! PGP-ENCODED emails preferred !! ___ 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 Manik Mayur Graduate student Microfluidics Lab Dept. of Mechanical Engg. IIT Kharagpur INDIA ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gm
Re: [gmx-users] problem in ngmx
Hi Justin, I tried maximum to find out the problem but i failed in that. I will give you the detailed steps..Kindly check once and tell me where is the problem. As you suggested now i am trying in gromacs 4.0.4 . 1. The ligand topology file is generated in PRODRG beta server using the GROMOS 96.1 force field. 2. The protein toplogy file using gromos 96 43 a1 force field 3. Tried to minimize in vacuum (Please find the em.mdp file). But the cycle finished at 15 steps. But in some previous post I saw that its not an error so I went ahead with genbox and further minimization. But ended in the same 15 th steps. also checked the gmxcheck for the files as you suggested it show the following error. '', 33685 atoms Last frame 0 time1.000 Both files read correctly Checking energy file 1RBP_water_min.edr --- Program gmxcheck, VERSION 4.0.4 Source code file: enxio.c, line: 283 Fatal error: Energy file 1RBP_water_min.edr not recognized, maybe different CPU? --- "I Do It All the Time" (Magnapop) Am I doing any mistake in the steps Please find some time to help me. Thank you very much, Aswathy Dept. Biotechnology Ext. 3108 - Original Message - From: "Justin A. Lemkul" To: "Discussion list for GROMACS users" Sent: Saturday, June 13, 2009 6:23:04 PM GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi Subject: Re: [gmx-users] problem in ngmx Ms. Aswathy S wrote: > Thank you very much for the reply... > > gmxcheck of my out shows a "segementation fault" in the last part. What > could be the problem?? > > this is the last part of the output > > x[31416] (-7.37978e-03 6.79718e+00 6.07531e+00) - (-7.4e-03 > 6.79720e+00 6.07530e+00) > x[31428] ( 2.35365e-01 -6.53947e-03 5.65519e+00) - ( 2.35400e-01 > -6.5e-03 5.65520e+00) > x[31478] ( 1.54478e-02 6.14019e+00 5.74537e+00) - ( 1.54000e-02 > 6.14020e+00 5.74540e+00) > Segmentation fault > > > The energy minimisation & the equilibration steps are finished at 15 step > eventhough it was given for 20 ps(1 steps).But the output coordinates > file doesnt show any abnornmality as i checked in the viewer? My > equilibration step was in NVT. > > whether nothing is happening or any other problem? > If you got 15 steps when you expected 10000, it seems pretty clear to me that something crashed very early on in your simulation. -Justin > Thanks & regards, > Aswathy > > > > > Dept. Biotechnology > Ext. 3108 > > - Original Message - > From: "Manik Mayur" > To: "Discussion list for GROMACS users" , > jalem...@vt.edu > Sent: Saturday, June 13, 2009 5:34:08 PM GMT +05:30 Chennai, Kolkata, Mumbai, > New Delhi > Subject: Re: [gmx-users] problem in ngmx > > > > > On Sat, Jun 13, 2009 at 5:14 PM, Florian Dommert < > domm...@icp.uni-stuttgart.de > wrote: > > > * Justin A. Lemkul < jalem...@vt.edu > [2009-06-13 07:31:17 -0400]: > > > > > > > Ms. Aswathy S wrote: > > > Hi, > > after equlibration of my protein and ligand I tried to create the energy file > ans well as the to display the trajectories using ngmx option,. But it shows > the follo: error, > > Xlib: connection to ":0.0" refused by server > Xlib: No protocol specified > > Can't connect to X Server. > Check your DISPLAY environment variable > > > Seems like your X environment is somehow not properly configured. > > > If you are working through ssh, then you can : > > $export DISPLAY=:0.0 > > > > Or you are tunneling through a SSH connection. There are several > possiblities: > > 1. Try ssh -X to login, this could solve the problem, if you are in > principle allowed to use X11 tunneling. > 2. In case this does not work either it can be that you are not allowed > to tunnel X11. > > However take care that you also need a properly configured XServer > running on your own system not just on the host you login. So in case > you use Windows or MacOS make sure this is the case. > > Flo > > > > > > > > > > > > > also the g_energy command shows that , > > Program g_energy_mpi, VERSION 3.3.3 > Source code file: enxio.c, line: 239 > > Fatal error: > Energy file eq_2ps_ener.edr not recognized, maybe different CPU? > > > What does gmxcheck tell you about the file. Perhaps it has been corrupted in > some way. > > Also, you may want to work with a more current version (4.0.5) to u
Re: [gmx-users] problem in ngmx
Hi Justin, Thanks for the reply. Once again i tried to minimize the protein +ligand in vacuum. Also tried by varying the maximum force constant. But that too converged at the 15 th step (or lesser steps based on the Fmax). The em.mdp file i have attached here with. Please go through that once please and tell me because of any of these parameters, the system behaves odd??. I think you are correct that the itp file created by PRODRG need corrections. But how can I chek that is that the problem with that file or how can i rectify? Dept. Biotechnology Ext. 3108 - Original Message - From: "Justin A. Lemkul" To: "Discussion list for GROMACS users" Sent: Sunday, June 14, 2009 10:51:30 PM GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi Subject: Re: [gmx-users] problem in ngmx Ms. Aswathy S wrote: > Hi Justin, > > I tried maximum to find out the problem but i failed in that. > > I will give you the detailed steps..Kindly check once and tell me where is > the problem. As you suggested now i am trying in gromacs 4.0.4 . > 1. The ligand topology file is generated in PRODRG beta server using the > GROMOS 96.1 force field. > 2. The protein toplogy file using gromos 96 43 a1 force field > 3. Tried to minimize in vacuum (Please find the em.mdp file). But the cycle > finished at 15 steps. >But in some previous post I saw that its not an error so I went ahead with > genbox and further minimization. But ended in the same 15 th steps. > also checked the gmxcheck for the files as you suggested it show the > following error. > What is most important is not the number of steps necessarily, but that the potential energy converged to an appropriate value and you reached an Fmax below your target. Realize that using a topology straight from PRODRG is often not the best course. The charges and charge groups assigned by PRODRG often require manual modification and verification of the parameters. This could be a source of problem. It may be that there is some kind of bug, but before that can be proposed, you have to demonstrate that the preparation steps were successful (i.e., EM criteria of potential energy and Fmax). -Justin > '', 33685 atoms > Last frame 0 time1.000 > > Both files read correctly > Checking energy file 1RBP_water_min.edr > > > --- > Program gmxcheck, VERSION 4.0.4 > Source code file: enxio.c, line: 283 > > Fatal error: > Energy file 1RBP_water_min.edr not recognized, maybe different CPU? > --- > > "I Do It All the Time" (Magnapop) > > Am I doing any mistake in the steps Please find some time to help me. > > > > Thank you very much, > Aswathy > Dept. Biotechnology > Ext. 3108 > > - Original Message - > From: "Justin A. Lemkul" > To: "Discussion list for GROMACS users" > Sent: Saturday, June 13, 2009 6:23:04 PM GMT +05:30 Chennai, Kolkata, Mumbai, > New Delhi > Subject: Re: [gmx-users] problem in ngmx > > > > Ms. Aswathy S wrote: >> Thank you very much for the reply... >> >> gmxcheck of my out shows a "segementation fault" in the last part. What >> could be the problem?? >> >> this is the last part of the output >> >> x[31416] (-7.37978e-03 6.79718e+00 6.07531e+00) - (-7.4e-03 >> 6.79720e+00 6.07530e+00) >> x[31428] ( 2.35365e-01 -6.53947e-03 5.65519e+00) - ( 2.35400e-01 >> -6.5e-03 5.65520e+00) >> x[31478] ( 1.54478e-02 6.14019e+00 5.74537e+00) - ( 1.54000e-02 >> 6.14020e+00 5.74540e+00) >> Segmentation fault >> >> >> The energy minimisation & the equilibration steps are finished at 15 step >> eventhough it was given for 20 ps(1 steps).But the output coordinates >> file doesnt show any abnornmality as i checked in the viewer? My >> equilibration step was in NVT. >> >> whether nothing is happening or any other problem? >> > > If you got 15 steps when you expected 1, it seems pretty clear to me that > something crashed very early on in your simulation. > > -Justin > >> Thanks & regards, >> Aswathy >> >> >> >> >> Dept. Biotechnology >> Ext. 3108 >> >> - Original Message ----- >> From: "Manik Mayur" >> To: "Discussion list for GROMACS users" , >> jalem...@vt.edu >> Sent: Saturday, June 13, 2009 5:34:08 PM GMT +05:30 Chennai, Kolkata, >> Mumbai, New Delhi >> Subject: Re: [gmx-users] problem in ngmx >> >> >> >> >> On Sat, Jun 13, 2009 at 5:14 PM, Florian
Re: [gmx-users] problem in ngmx
hi justin, your suggestions were helpful. Actually charges in the ligand topology was having the problem. So I have added the charges from the antechamber. Did Energy minimization. Now did an NVT equilibration of 10 ps. It finished at 2600 steps. But shows reasonable Energy and Temperature (checked in the xmgrace). Seems it works fine..Now started the NPT equilibration. Thank you very much for your support. Aswathy Dept. Biotechnology Ext. 3108 - Original Message - From: "Justin A. Lemkul" To: "Discussion list for GROMACS users" Sent: Monday, June 15, 2009 4:58:20 PM GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi Subject: Re: [gmx-users] problem in ngmx Ms. Aswathy S wrote: > Hi Justin, > > Thanks for the reply. > > Once again i tried to minimize the protein +ligand in vacuum. Also tried by > varying the maximum force constant. But that too converged at the 15 th step > (or lesser steps based on the Fmax). The em.mdp file i have attached here > with. Please go through that once please and tell me because of any of these > parameters, the system behaves odd??. > As I said before, it is not the step that matters, it is whether or not the system converges within your criteria. I am assuming EM is working, based on the fact that the process converges differently depending on different target values for Fmax. Your .mdp file looks reasonable. If we can clarify for a moment - several messages ago you claimed that you were doing a 20-ps NVT equilibration that was finishing at 15 steps, but that appears to not be the case. Is it the NVT step that is failing to complete? Is ngmx failing to display the NVT trajectory, and did gmxcheck report problems with the .edr file? > I think you are correct that the itp file created by PRODRG need corrections. > But how can I chek that is that the problem with that file or how can i > rectify? > Parameterization is very difficult. Prepare for a lot of advanced work. Please see here: http://oldwiki.gromacs.org/index.php/Parameterization -Justin > Dept. Biotechnology Ext. 3108 > > - Original Message - From: "Justin A. Lemkul" To: > "Discussion list for GROMACS users" Sent: Sunday, > June 14, 2009 10:51:30 PM GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi > Subject: Re: [gmx-users] problem in ngmx > > > > Ms. Aswathy S wrote: >> Hi Justin, >> >> I tried maximum to find out the problem but i failed in that. >> >> I will give you the detailed steps..Kindly check once and tell me where is >> the problem. As you suggested now i am trying in gromacs 4.0.4 . 1. The >> ligand topology file is generated in PRODRG beta server using the GROMOS >> 96.1 force field. 2. The protein toplogy file using gromos 96 43 a1 force >> field 3. Tried to minimize in vacuum (Please find the em.mdp file). But the >> cycle finished at 15 steps. But in some previous post I saw that its not >> an error so I went ahead with genbox and further minimization. But ended in >> the same 15 th steps. also checked the gmxcheck for the files as you >> suggested it show the following error. >> > > What is most important is not the number of steps necessarily, but that the > potential energy converged to an appropriate value and you reached an Fmax > below your target. > > Realize that using a topology straight from PRODRG is often not the best > course. The charges and charge groups assigned by PRODRG often require manual > modification and verification of the parameters. This could be a source of > problem. > > It may be that there is some kind of bug, but before that can be proposed, > you have to demonstrate that the preparation steps were successful (i.e., EM > criteria of potential energy and Fmax). > > -Justin > >> '', 33685 atoms Last frame 0 time1.000 >> >> Both files read correctly Checking energy file 1RBP_water_min.edr >> >> >> --- Program gmxcheck, >> VERSION 4.0.4 Source code file: enxio.c, line: 283 >> >> Fatal error: Energy file 1RBP_water_min.edr not recognized, maybe different >> CPU? --- >> >> "I Do It All the Time" (Magnapop) >> >> Am I doing any mistake in the steps Please find some time to help me. >> >> >> >> Thank you very much, Aswathy Dept. Biotechnology Ext. 3108 >> >> - Original Message - From: "Justin A. Lemkul" To: >> "Discussion list for GROMACS users" Sent: >> Saturday, June 13, 2009 6:23:04 PM GMT +05:30 Chennai, Kolkata, Mumbai, New >&g
Re: [gmx-users] problem in ngmx
Hi,
In my NPT step I think there is some poblem. i am getting the follo: error. I
have used box as cubic I s that could be the problem Please see the
md,..mop file
Please try to hepl me..
Box[2]={ nan, nan, nan}
Can not fix pbc.
Warning: Only triclinic boxes with the first vector parallel to the x-axis and
the second vector in the xy-plane are supported.
Box (3x3):
Box[0]={ nan, nan, nan}
Box[1]={ nan, nan, nan}
Box[2]={ nan, nan, nan}
Can not fix pbc.
Warning: Only triclinic boxes with the first vector parallel to the x-axis and
the second vector in the xy-plane are supported.
Box (3x3):
Box[0]={ nan, nan, nan}
Box[1]={ nan, nan, nan}
Box[2]={ nan, nan, nan}
Can not fix pbc.
Warning: Only triclinic boxes with the first vector parallel to the x-axis and
the second vector in the xy-plane are supported.
Box (3x3):
Box[0]={ nan, nan, nan}
Box[1]={ nan, nan, nan}
Box[2]={ nan, nan, nan}
Can not fix pbc.
Warning: Only triclinic boxes with the first vector parallel to the x-axis and
the second vector in the xy-plane are supported.
Box (3x3):
Box[0]={ nan, nan, nan}
Box[1]={ nan, nan, nan}
Box[2]={ nan, nan, nan}
Can not fix pbc.
---
Program mdrun, VERSION 4.0.4
Source code file: nsgrid.c, line: 348
Fatal error:
Number of grid cells is zero. Probably the system and box collapsed.
---
"Would You Like to Be the Monster Tonight ?" (Captain Beefheart)
OIn some pev
Dept. Biotechnology
Ext. 3108
- Original Message -
From: "Ms. Aswathy S"
To: "Discussion list for GROMACS users"
Sent: Tuesday, June 16, 2009 12:40:04 PM GMT +05:30 Chennai, Kolkata, Mumbai,
New Delhi
Subject: Re: [gmx-users] problem in ngmx
hi justin,
your suggestions were helpful. Actually charges in the ligand topology was
having the problem. So I have added the charges from the antechamber. Did
Energy minimization. Now did an NVT equilibration of 10 ps. It finished at 2600
steps. But shows reasonable Energy and Temperature (checked in the xmgrace).
Seems it works fine..Now started the NPT equilibration.
Thank you very much for your support.
Aswathy
Dept. Biotechnology
Ext. 3108
- Original Message -
From: "Justin A. Lemkul"
To: "Discussion list for GROMACS users"
Sent: Monday, June 15, 2009 4:58:20 PM GMT +05:30 Chennai, Kolkata, Mumbai, New
Delhi
Subject: Re: [gmx-users] problem in ngmx
Ms. Aswathy S wrote:
> Hi Justin,
>
> Thanks for the reply.
>
> Once again i tried to minimize the protein +ligand in vacuum. Also tried by
> varying the maximum force constant. But that too converged at the 15 th step
> (or lesser steps based on the Fmax). The em.mdp file i have attached here
> with. Please go through that once please and tell me because of any of these
> parameters, the system behaves odd??.
>
As I said before, it is not the step that matters, it is whether or not the
system converges within your criteria. I am assuming EM is working, based on
the fact that the process converges differently depending on different target
values for Fmax. Your .mdp file looks reasonable.
If we can clarify for a moment - several messages ago you claimed that you were
doing a 20-ps NVT equilibration that was finishing at 15 steps, but that
appears
to not be the case. Is it the NVT step that is failing to complete? Is ngmx
failing to display the NVT trajectory, and did gmxcheck report problems with
the
.edr file?
> I think you are correct that the itp file created by PRODRG need corrections.
> But how can I chek that is that the problem with that file or how can i
> rectify?
>
Parameterization is very difficult. Prepare for a lot of advanced work.
Please
see here:
http://oldwiki.gromacs.org/index.php/Parameterization
-Justin
> Dept. Biotechnology Ext. 3108
>
> - Original Message - From: "Justin A. Lemkul" To:
> "Discussion list for GROMACS users" Sent: Sunday,
> June 14, 2009 10:51:30 PM GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi
> Subject: Re: [gmx-users] problem in ngmx
>
>
>
> Ms. Aswathy S wrote:
>> Hi Justin,
>>
>> I tried maximum to find out the problem but i failed in that.
>>
Re: [gmx-users] problem in ngmx
sorry..forgot to attach the file...
After my NVT I have checked the PE of the system..It was stabilised..So I
thought everything was fine till NVT. How can i check whetehr its a problem
with NVT?Is that the box type could be the resaon?
Dept. Biotechnology
Ext. 3108
- Original Message -
From: "Justin A. Lemkul"
To: "Discussion list for GROMACS users"
Sent: Tuesday, June 16, 2009 4:44:47 PM GMT +05:30 Chennai, Kolkata, Mumbai,
New Delhi
Subject: Re: [gmx-users] problem in ngmx
Ms. Aswathy S wrote:
> Hi,
>
> In my NPT step I think there is some poblem. i am getting the follo: error. I
> have used box as cubic I s that could be the problem Please see the
> md,..mop file
>
You haven't posted the .mdp file. In any case, see my previous message. I
think something went wrong during NVT. Here, the messages indicate that your
box is exploding. See, for example:
http://oldwiki.gromacs.org/index.php/blowing_up
-Justin
> Please try to hepl me.. Box[2]={ nan, nan, nan}
> Can not fix pbc. Warning: Only triclinic boxes with the first vector
> parallel to the x-axis and the second vector in the xy-plane are supported.
> Box (3x3): Box[0]={ nan, nan, nan} Box[1]={
> nan, nan, nan} Box[2]={ nan, nan,
> nan} Can not fix pbc. Warning: Only triclinic boxes with the first vector
> parallel to the x-axis and the second vector in the xy-plane are supported.
> Box (3x3): Box[0]={ nan, nan, nan} Box[1]={
> nan, nan, nan} Box[2]={ nan, nan,
> nan} Can not fix pbc. Warning: Only triclinic boxes with the first vector
> parallel to the x-axis and the second vector in the xy-plane are supported.
> Box (3x3): Box[0]={ nan, nan, nan} Box[1]={
> nan, nan, nan} Box[2]={ nan, nan,
> nan} Can not fix pbc. Warning: Only triclinic boxes with the first vector
> parallel to the x-axis and the second vector in the xy-plane are supported.
> Box (3x3): Box[0]={ nan, nan, nan} Box[1]={
> nan, nan, nan} Box[2]={ nan, nan,
> nan} Can not fix pbc.
>
> --- Program mdrun,
> VERSION 4.0.4 Source code file: nsgrid.c, line: 348
>
> Fatal error: Number of grid cells is zero. Probably the system and box
> collapsed.
>
> ---
>
> "Would You Like to Be the Monster Tonight ?" (Captain Beefheart)
>
>
> OIn some pev Dept. Biotechnology Ext. 3108
>
> - Original Message - From: "Ms. Aswathy S"
> To: "Discussion list for GROMACS users"
> Sent: Tuesday, June 16, 2009 12:40:04 PM GMT +05:30
> Chennai, Kolkata, Mumbai, New Delhi Subject: Re: [gmx-users] problem in ngmx
>
> hi justin,
>
> your suggestions were helpful. Actually charges in the ligand topology was
> having the problem. So I have added the charges from the antechamber. Did
> Energy minimization. Now did an NVT equilibration of 10 ps. It finished at
> 2600 steps. But shows reasonable Energy and Temperature (checked in the
> xmgrace). Seems it works fine..Now started the NPT equilibration.
>
> Thank you very much for your support.
>
> Aswathy Dept. Biotechnology Ext. 3108
>
> - Original Message - From: "Justin A. Lemkul" To:
> "Discussion list for GROMACS users" Sent: Monday,
> June 15, 2009 4:58:20 PM GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi
> Subject: Re: [gmx-users] problem in ngmx
>
>
>
> Ms. Aswathy S wrote:
>> Hi Justin,
>>
>> Thanks for the reply.
>>
>> Once again i tried to minimize the protein +ligand in vacuum. Also tried by
>> varying the maximum force constant. But that too converged at the 15 th
>> step (or lesser steps based on the Fmax). The em.mdp file i have attached
>> here with. Please go through that once please and tell me because of any of
>> these parameters, the system behaves odd??.
>>
>
> As I said before, it is not the step that matters, it is whether or not the
> system converges within your criteria. I am assuming EM is working, based on
> the fact that the process converges differently depending on different
> target values for Fmax. Your .mdp file looks reasonable.
>
> If we can clarify for a moment - several messages ago you claimed that you
> were doing a 20-ps NVT equilibration that was finishing at 15 steps, but that
> appears to not be the case. Is it the NVT step that is failing to complete?
> Is ngmx failing to
Re: [gmx-users] problem in ngmx
My point was I have set the NVT equilibration as 10 ps. But it run only 5.4 ps.
when I checked the temperature It was also stabilized at 5.4 ps. That is why I
went ahead with NPT.Can we consider OK, if the equilibration stops before the
time we set??
I am following some literatures, from that i thought first I should equlibrate
the water then give restraint to water and equilibrate the protein further.
thats why I did in that way???I will check that once again.
Dept. Biotechnology
Ext. 3108
- Original Message -
From: "Justin A. Lemkul"
To: "Gromacs Users' List"
Sent: Tuesday, June 16, 2009 5:03:26 PM GMT +05:30 Chennai, Kolkata, Mumbai,
New Delhi
Subject: Re: [gmx-users] problem in ngmx
Ms. Aswathy S wrote:
> sorry..forgot to attach the file...
>
> After my NVT I have checked the PE of the system..It was stabilised..So I
> thought everything was fine till NVT. How can i check whetehr its a problem
> with NVT?Is that the box type could be the resaon?
>
>
Convergence of PE is a good indicator that energy minimization is complete.
The
purpose of NVT is to stabilize the temperature of the system. My main problem
with what you said before was that you did 10 ps of NVT in 2600 steps. This
seems wrong, given the fractional nature of the time step required to do such a
procedure. Use gmxcheck on the .trr or .edr file to see how many frames it
finds; verify that you have a complete trajectory.
Also, in the .mdp file you attached, you are applying position restraints to
the
water in your system. If you are not also restraining the protein, it is
probably colliding with the water, causing the explosion you are seeing. Why
are you restraining water during NPT equilibration, or during MD for that
matter?
-Justin
> Dept. Biotechnology Ext. 3108
>
> - Original Message - From: "Justin A. Lemkul" To:
> "Discussion list for GROMACS users" Sent: Tuesday,
> June 16, 2009 4:44:47 PM GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi
> Subject: Re: [gmx-users] problem in ngmx
>
>
>
> Ms. Aswathy S wrote:
>> Hi,
>>
>> In my NPT step I think there is some poblem. i am getting the follo: error.
>> I have used box as cubic I s that could be the problem Please see the
>> md,..mop file
>>
>
> You haven't posted the .mdp file. In any case, see my previous message. I
> think something went wrong during NVT. Here, the messages indicate that your
> box is exploding. See, for example:
>
> http://oldwiki.gromacs.org/index.php/blowing_up
>
> -Justin
>
>> Please try to hepl me.. Box[2]={ nan, nan,
>> nan} Can not fix pbc. Warning: Only triclinic boxes with the first vector
>> parallel to the x-axis and the second vector in the xy-plane are supported.
>> Box (3x3): Box[0]={ nan, nan, nan} Box[
>> 1]={ nan, nan, nan} Box[2]={ nan,
>> nan, nan} Can not fix pbc. Warning: Only triclinic boxes with the first
>> vector parallel to the x-axis and the second vector in the xy-plane are
>> supported. Box (3x3): Box[0]={ nan, nan, nan}
>> Box[1]={ nan, nan, nan} Box[2]={ nan,
>> nan, nan} Can not fix pbc. Warning: Only triclinic boxes with the first
>> vector parallel to the x-axis and the second vector in the xy-plane are
>> supported. Box (3x3): Box[0]={ nan, nan, nan}
>> Box[1]={ nan, nan, nan} Box[2]={ nan,
>> nan, nan} Can not fix pbc. Warning: Only triclinic boxes with the first
>> vector parallel to the x-axis and the second vector in the xy-plane are
>> supported. Box (3x3): Box[0]={ nan, nan, nan}
>> Box[1]={ nan, nan, nan} Box[2]={ nan,
>> nan, nan} Can not fix pbc.
>>
>> --- Program mdrun,
>> VERSION 4.0.4 Source code file: nsgrid.c, line: 348
>>
>> Fatal error: Number of grid cells is zero. Probably the system and box
>> collapsed.
>>
>> ---
>>
>> "Would You Like to Be the Monster Tonight ?" (Captain Beefheart)
>>
>>
>> OIn some pev Dept. Biotechnology Ext. 3108
>>
>> - Original Message - From: "Ms. Aswathy S"
>> To: "Discussion list for GROMACS users"
>> Sent: Tuesday, June 16, 2009 12:40:04 PM GMT +05:30
>> Chennai, Kolkata, Mumbai, New Delhi Subject: Re: [gmx-users] problem in
>> ngmx
>>
>> hi justin,
>>
>> your suggestions were
Re: [gmx-users] problem in ngmx
hi Justin,
I tried the NVT once with certain changes in the parameter file. Now its
finished the 10 ps. But I have used the charge as the same from the antechamber
program. Do you think the result will be reliable? Please check the mdp file
attached for NVT.
Thnaks for your help
Aswathy
Dept. Biotechnology
Ext. 3108
- Original Message -
From: "Justin A. Lemkul"
To: "Gromacs Users' List"
Sent: Tuesday, June 16, 2009 5:29:46 PM GMT +05:30 Chennai, Kolkata, Mumbai,
New Delhi
Subject: Re: [gmx-users] problem in ngmx
Ms. Aswathy S wrote:
> My point was I have set the NVT equilibration as 10 ps. But it run only 5.4
> ps. when I checked the temperature It was also stabilized at 5.4 ps. That is
> why I went ahead with NPT.Can we consider OK, if the equilibration stops
> before the time we set??
>
Absolutely not. If any MD process stops before it is supposed to, that means
it
crashed.
>
> I am following some literatures, from that i thought first I should
> equlibrate the water then give restraint to water and equilibrate the
> protein further. thats why I did in that way???I will check that once again.
>
Not necessary. In all the recent literature I have seen, position restraints
are placed on the protein, while the solvent is free to move. After some time,
all restraints are removed and production MD is conducted.
In any case, your problem occurs before you get to this stage. Your NVT is
failing; you need to figure out why.
-Justin
>
>
> Dept. Biotechnology Ext. 3108
>
> - Original Message - From: "Justin A. Lemkul" To:
> "Gromacs Users' List" Sent: Tuesday, June 16, 2009
> 5:03:26 PM GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi Subject: Re:
> [gmx-users] problem in ngmx
>
>
>
> Ms. Aswathy S wrote:
>> sorry..forgot to attach the file...
>>
>> After my NVT I have checked the PE of the system..It was stabilised..So I
>> thought everything was fine till NVT. How can i check whetehr its a problem
>> with NVT?Is that the box type could be the resaon?
>>
>>
>
> Convergence of PE is a good indicator that energy minimization is complete.
> The purpose of NVT is to stabilize the temperature of the system. My main
> problem with what you said before was that you did 10 ps of NVT in 2600
> steps. This seems wrong, given the fractional nature of the time step
> required to do such a procedure. Use gmxcheck on the .trr or .edr file to
> see how many frames it finds; verify that you have a complete trajectory.
>
> Also, in the .mdp file you attached, you are applying position restraints to
> the water in your system. If you are not also restraining the protein, it is
> probably colliding with the water, causing the explosion you are seeing.
> Why are you restraining water during NPT equilibration, or during MD for that
> matter?
>
> -Justin
>
>> Dept. Biotechnology Ext. 3108
>>
>> - Original Message - From: "Justin A. Lemkul" To:
>> "Discussion list for GROMACS users" Sent: Tuesday,
>> June 16, 2009 4:44:47 PM GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi
>> Subject: Re: [gmx-users] problem in ngmx
>>
>>
>>
>> Ms. Aswathy S wrote:
>>> Hi,
>>>
>>> In my NPT step I think there is some poblem. i am getting the follo:
>>> error. I have used box as cubic I s that could be the problem Please
>>> see the md,..mop file
>>>
>> You haven't posted the .mdp file. In any case, see my previous message. I
>> think something went wrong during NVT. Here, the messages indicate that
>> your box is exploding. See, for example:
>>
>> http://oldwiki.gromacs.org/index.php/blowing_up
>>
>> -Justin
>>
>>> Please try to hepl me.. Box[2]={ nan, nan, nan} Can
>>> not fix pbc. Warning: Only triclinic boxes with the first vector parallel
>>> to the x-axis and the second vector in the xy-plane are supported. Box
>>> (3x3): Box[0]={ nan, nan, nan} Box[ 1]={
>>> nan, nan, nan} Box[2]={ nan, nan, nan} Can
>>> not fix pbc. Warning: Only triclinic boxes with the first vector parallel
>>> to the x-axis and the second vector in the xy-plane are supported. Box
>>> (3x3): Box[0]={ nan, nan, nan} Box[1]={
>>> nan, nan, nan} Box[2]={ nan, nan, nan} Can
>>> not fix pbc. Warning: Only triclinic boxes with the first vector parallel
>>> to the x-axis and the second vector in the xy-plane are s
Re: [gmx-users] problem in ngmx
Ok. You meant I have to cross check these parameters before getting in to simulation.I will do that Thank you very much for your replies. Dept. Biotechnology Ext. 3108 - Original Message - From: "Justin A. Lemkul" To: "Discussion list for GROMACS users" Sent: Wednesday, June 17, 2009 6:35:01 PM GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi Subject: Re: [gmx-users] problem in ngmx Marc F. Lensink wrote: > On Wed, Jun 17, 2009 at 06:57:24AM -0400, Justin A. Lemkul wrote: >> The .mdp file seems reasonable. QM charges are not necessarily the end >> result in Gromos parameterization. In fact, such calculations are often >> unnecessary. In my experience, assigning charges based on functional groups >> already present in the force field is often a reasonable starting point. >> But in any case, you must always verify your results and, in the end, >> follow the same parameterization scheme as the original force field (which, >> in the case of the Gromos force fields, does not include QM charge >> calculations). > > I've run hundreds of QM charge calculations. in many cases, they are > remarkably similar to the gromos charges... > Agreed. The point I was trying to make (perhaps poorly) was that simply running a QM charge calculation and calling it done is not the right track. I got the impression from the original post that charges were assigned and a simulation conducted without any validation of those parameters. -Justin > cheers, > marc > ___ > 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 ___ 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] Coordinates change after minimization
Hi, After minimizing the protein -ligand complex, the co-ordinates have changed drastically.My idea about minimization was the coordinates will have minute changes only. In this case my protein is completely transferring to a new co-ordinates.Is that reasonable.?? Thanks, Aswathy Dept. Biotechnology Ext. 3108 ___ 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] Coordinates change after minimization
using the g_confrm command the RMSD of the protein is 0 (Root mean square deviation after lsq fit = 4.14581e-08). It means the structure doesn't have a major change ultimately.. Please correct me if I am wrong..Can I move ahead with this minimization? Dept. Biotechnology Ext. 3108 - Original Message - From: "David van der Spoel" To: "Discussion list for GROMACS users" Sent: Saturday, June 20, 2009 6:07:20 PM GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi Subject: Re: [gmx-users] Coordinates change after minimization Justin A. Lemkul wrote: > > > Ms. Aswathy S wrote: >> Hi, >> >> After minimizing the protein -ligand complex, the co-ordinates have >> changed >> drastically.My idea about minimization was the coordinates will have >> minute >> changes only. In this case my protein is completely transferring to a new >> co-ordinates.Is that reasonable.?? > > The amount of change will depend on the quality of the initial model. > If large changes need to be made, they can be. If the entire protein is > moving, then perhaps the box has not been prepared correctly, and the > translation is caused by a periodic jump. Have a look at the output > (not just the coordinates) and see if you can deduce what's going on. > Try running g_confrms to see whether they really are very different. > -Justin > >> >> Thanks, Aswathy Dept. Biotechnology Ext. 3108 >> ___ 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 >> > -- David. David van der Spoel, PhD, Professor of Biology Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 sp...@xray.bmc.uu.sesp...@gromacs.org http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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 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] Coordinates change after minimization
But i am in a situation like the minimization doesn't make any change in the energy and it convergeing at 15 th step each time. So further minimization is not possible. Can you plz check the em.mdp file and tell me whetehr I have given any wrong parameter? Dept. Biotechnology Ext. 3108 - Original Message - From: "XAvier Periole" To: "Discussion list for GROMACS users" Sent: Saturday, June 20, 2009 7:16:26 PM GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi Subject: Re: [gmx-users] Coordinates change after minimization On Jun 20, 2009, at 15:30, "Ms. Aswathy S" wrote: > using the g_confrm command the RMSD of the protein is 0 (Root mean > square deviation after lsq fit = 4.14581e-08). It means the > structure doesn't have a major change ultimately.. Please correct me > if I am wrong.. You are correct. > Can I move ahead with this minimization? However this value is really small, which suggests that the minimization did actually about nothing. This a bit too nothing! Of I were you I would check that you actually used g_confrm the right way or indeed performed a minization. > > Dept. Biotechnology > Ext. 3108 > > - Original Message - > From: "David van der Spoel" > To: "Discussion list for GROMACS users" > Sent: Saturday, June 20, 2009 6:07:20 PM GMT +05:30 Chennai, > Kolkata, Mumbai, New Delhi > Subject: Re: [gmx-users] Coordinates change after minimization > > Justin A. Lemkul wrote: >> >> >> Ms. Aswathy S wrote: >>> Hi, >>> >>> After minimizing the protein -ligand complex, the co-ordinates have >>> changed >>> drastically.My idea about minimization was the coordinates will have >>> minute >>> changes only. In this case my protein is completely transferring >>> to a new >>> co-ordinates.Is that reasonable.?? >> >> The amount of change will depend on the quality of the initial model. >> If large changes need to be made, they can be. If the entire >> protein is >> moving, then perhaps the box has not been prepared correctly, and the >> translation is caused by a periodic jump. Have a look at the output >> (not just the coordinates) and see if you can deduce what's going on. >> > Try running g_confrms to see whether they really are very different. > >> -Justin >> >>> >>> Thanks, Aswathy Dept. Biotechnology Ext. 3108 >>> ___ 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 >>> >> > > > -- > David. > > David van der Spoel, PhD, Professor of Biology > Dept. of Cell and Molecular Biology, Uppsala University. > Husargatan 3, Box 596, 75124 Uppsala, Sweden > phone:46 18 471 4205fax: 46 18 511 755 > sp...@xray.bmc.uu.sesp...@gromacs.org http://folding.bmc.uu.se > + > +++ > ___ > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/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 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 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 em_old.mdp 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
[gmx-users] few doubts regarding 1-4 interaction
Hi gromacs users, I am facing the same error during Production run that faced by so many gromacs users and I know this query has been answered for several times. But Could you please tell me some specific doubt regarding the 1-4 interaction error that usually occurs? I have equilibrated my protein ligand system of around 600 ps and shown a satisfied level of equilibration. Then I moved to the Production run of 3ns. But shows the same 1-4 interaction error. My doubts are, 1. It was advised by gromacs experts that better I should go for another round of minimization. Is it on the equilibrated structure? 2. If so Do i need to equilibrate again after minimization? 3. I have did 2500 steps of minimization on the structure which is equilibrated and then again run for 3ns production run But occured the same error at 3 lakh step? if I reduce my time step how that will affect this error(I have seen in the error section of gromacs that another possibility is to reduce the time step?) Can you please tell me your suggestion on these?? Thank you. Aswathy Dept. Biotechnology Ext. 3108 ___ 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] few doubts regarding 1-4 interaction
Thanks Justin. I am trying to do the simulation of protein-ligand complex. 1. Minimized the protein(but converged before the Fmax reached the threshold) 2. Did a 50 steps of NVT equilibration 3. Then an NPT equilibration reached at 650 steps (checked the RMSD with the initial structure) 4. Then tried to do a 3 ns production run. But failed ~ after 170 ps. I am attching the NPT file I have used for equilibration. Also the structure after equilibration does not have any clashes or bad contact in the rough analysis. How can I do a more close checking of this? Once again Thank you for your response. Aswathy - Original Message - From: "Justin A. Lemkul" To: "Discussion list for GROMACS users" Sent: Tuesday, June 30, 2009 8:33:19 PM GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi Subject: Re: [gmx-users] few doubts regarding 1-4 interaction Ms. Aswathy S wrote: > Hi gromacs users, > > I am facing the same error during Production run that faced by so many > gromacs users and I know this query has been answered for several times. But > Could you please tell me some specific doubt regarding the 1-4 interaction > error that usually occurs? > > I have equilibrated my protein ligand system of around 600 ps and shown a > satisfied level of equilibration. Then I moved to the Production run of 3ns. > But shows the same 1-4 interaction error. My doubts are, > > 1. It was advised by gromacs experts that better I should go for another > round of minimization. Is it on the equilibrated structure? It would be good if you could remind us of what you are doing, as well as cite the actual post where you were told to do this. > 2. If so Do i need to equilibrate again after minimization? Yes. > 3. I have did 2500 steps of minimization on the structure which is > equilibrated and then again run for 3ns production run But occured the same > error at 3 lakh step? if I reduce my time step how that will affect this > error(I have seen in the error section of gromacs that another possibility is > to reduce the time step?) Reducing the timestep can in some cases finesse the problem into behaving. If there is something more deeply wrong with your model, then this probably won't help out a whole lot. If you can post a more complete description of what it is you are doing, what parameters you are using, etc. you might get more detailed suggestions. The bottom line is, if your system is blowing up, something about the model physics is unreasonable. -Justin > Can you please tell me your suggestion on these?? > > Thank you. Aswathy > > Dept. Biotechnology Ext. 3108 ___ > 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 md_NPT.mdp 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
[gmx-users] Water atoms cannot be settled
Hi , I am doing a protein ligand Md simulation. 1. I did the energy minimization 2. A 500 ps NVT equilibration 3. then a 1 ns NPT simulation , and seemed that the system is equilibrated enough I went ahead with Md run for 5 ns. But at the step of 7 I got the error like "Some of the water atoms cannot be settled." I understood that some water molecules making bas contacts/ or clashes. But How can I rectify that ? Do I need to continue with equilibration again? or any tother way to get out of this problem"? Attaching the equilibration parameter files here with . Please tell me your comments, Thanks Aswathy Dept. Biotechnology Ext. 3108 md_Eq1_NVT.mdp Description: Binary data md_NPT.mdp 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] Water atoms cannot be settled
Thank you for your quick response. I am trying all these possibilities. Can you please make me one thing clear, In certain papers and tutorials it is seen that , for production run they are using either NPT or NVT. Which one should i try for my protein ligand complex.(Right now I did NVT condition) attaching the mdp file. Thanks & Regards, Aswathy Dept. Biotechnology Ext. 3108 - Original Message - From: "Mark Abraham" To: "Discussion list for GROMACS users" Sent: Wednesday, July 8, 2009 5:27:42 PM GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi Subject: Re: [gmx-users] Water atoms cannot be settled Ms. Aswathy S wrote: > Hi , > > I am doing a protein ligand Md simulation. > > 1. I did the energy minimization > 2. A 500 ps NVT equilibration > 3. then a 1 ns NPT simulation , and seemed that the system is equilibrated > enough I went ahead with Md run for 5 ns. > > But at the step of 7 I got the error like "Some of the water atoms cannot > be settled." I understood that some water molecules making bas contacts/ or > clashes. But How can I rectify that ? Do I need to continue with > equilibration again? or any tother way to get out of this problem"? > > Attaching the equilibration parameter files here with . > Please tell me your comments, Thanks You can try removing your position restraints before you change the ensemble to NPT. Also you should inspect the trajectory visually to see whether you can deduce what the problem is from its symptoms. Further, look to see how much your box size is changing when you switch to NPT. You'd prefer it didn't change a great deal - and if it does, equilibrating longer is likely to be needed. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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 md_final.mdp 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
[gmx-users] IN4 molecule type error
Dear Gromacs users, I am a new user of gromacs. I was trying the Enzyme- Drug complex tutorial for a test run and i have ended up with following error. Please try to help me creating statusfile for 1 node... Back Off! I just backed up mdout.mdp to ./#mdout.mdp.90# checking input for internal consistency... calling /usr/bin/cpp... TEST1/trp.top:12:9: error: #include expects "FILENAME" or cpp exit code: 256 Tried to execute: '/usr/bin/cpp -I/usr/local/gromacs/share/top -DFLEXIBLE TEST1/trp.top > gromppVEFM2b' The '/usr/bin/cpp' command is defined in the .mdp file processing topology... Generated 1284 of the 1485 non-bonded parameter combinations Excluding 3 bonded neighbours for Protein_A 1 Cleaning up temporary file gromppVEFM2b Fatal error: No such moleculetype IN4 Can you please tell me what could be the reason for this? Please help me. Thanks in advance, Aswathy Amrita School of Biotechnology Dept. Biotechnology Ext. 3108 ___ 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: gmx-users Digest, Vol 58, Issue 2
Dear Mohammed, Thanks for your reply. The .ITP file from the PRODRG server has saved as drg.itp and added "#include "drg.itp"" line in the topology file. still getting the same error. Where should I save the drg.itp file in the present working directory or share/top directory? Thanks, Aswathy Dept. Biotechnology Ext. 3108 - Original Message - From: gmx-users-requ...@gromacs.org To: gmx-users@gromacs.org Sent: Sunday, February 1, 2009 4:30:04 PM GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi Subject: gmx-users Digest, Vol 58, Issue 2 Send gmx-users mailing list submissions to gmx-users@gromacs.org To subscribe or unsubscribe via the World Wide Web, visit http://www.gromacs.org/mailman/listinfo/gmx-users or, via email, send a message with subject or body 'help' to gmx-users-requ...@gromacs.org You can reach the person managing the list at gmx-users-ow...@gromacs.org When replying, please edit your Subject line so it is more specific than "Re: Contents of gmx-users digest..." Today's Topics: 1. RE: IN4 molecule type error (Mohammed Kamal) -- Message: 1 Date: Sun, 1 Feb 2009 21:11:11 +1100 From: Mohammed Kamal Subject: RE: [gmx-users] IN4 molecule type error To: Gromacs Message-ID: Content-Type: text/plain; charset="iso-8859-1" You have to include the .itp file that you have obtained from PRODRG in the topology file. Be sure that you have changed the extension of the .itp file that you have obtained from the PRODRG server from .ITP to .itp!! Mohammed > Date: Fri, 30 Jan 2009 20:57:28 +0530 > From: aswat...@amritapuri.amrita.edu > To: gmx-users@gromacs.org > Subject: [gmx-users] IN4 molecule type error > > Dear Gromacs users, > > I am a new user of gromacs. I was trying the Enzyme- Drug complex tutorial > for a test run and i have ended up with following error. Please try to help me > > > creating statusfile for 1 node... > > Back Off! I just backed up mdout.mdp to ./#mdout.mdp.90# > checking input for internal consistency... > calling /usr/bin/cpp... > TEST1/trp.top:12:9: error: #include expects "FILENAME" or > cpp exit code: 256 > Tried to execute: '/usr/bin/cpp -I/usr/local/gromacs/share/top -DFLEXIBLE > TEST1/trp.top > gromppVEFM2b' > The '/usr/bin/cpp' command is defined in the .mdp file > processing topology... > Generated 1284 of the 1485 non-bonded parameter combinations > Excluding 3 bonded neighbours for Protein_A 1 > Cleaning up temporary file gromppVEFM2b > Fatal error: No such moleculetype IN4 > > Can you please tell me what could be the reason for this? Please help me. > > Thanks in advance, > > Aswathy > Amrita School of Biotechnology > Dept. Biotechnology > Ext. 3108 > ___ > 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 _ Get rid of those unwanted christmas presents! Get what you want at ebay. http://a.ninemsn.com.au/b.aspx?URL=http%3A%2F%2Frover%2Eebay%2Ecom%2Frover%2F1%2F705%2D10129%2D5668%2D323%2F4%3Fid%3D10&_t=763807330&_r=hotmailTAGLINES&_m=EXT -- next part -- An HTML attachment was scrubbed... URL: http://www.gromacs.org/pipermail/gmx-users/attachments/20090201/800342b2/attachment-0001.html -- ___ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! End of gmx-users Digest, Vol 58, Issue 2 ___ 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: IN4 molecule type error
Hi, I have added the #include "drg.itp" statement under the title, ; Include forcefield parameters in the .top file. Thr drg.itp is saved in the current directory. Still showing the sanme error as previous. including a part of the top file.Please check this. ; This is your topology file ; TRYPSIN ; ; Include forcefield parameters #include "ffgmx.itp" #include "drg.itp" [ moleculetype ] ; Namenrexcl Protein_A 3 At the end, ; Include Position restraint file #ifdef POSRES #include "posre.itp" #endif ; Include water topology #include "spce.itp" #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ; Include generic topology for ions #include "ions.itp" [ system ] ; Name TRYPSIN in water [ molecules ] ; Compound#mols Protein_A 1 IN4 1 SOL 8902 ___ Thanks, Aswathy Dept. Biotechnology Ext. 3108 - Original Message - From: gmx-users-requ...@gromacs.org To: gmx-users@gromacs.org Sent: Sunday, February 1, 2009 9:28:44 PM GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi Subject: gmx-users Digest, Vol 58, Issue 3 Send gmx-users mailing list submissions to gmx-users@gromacs.org To subscribe or unsubscribe via the World Wide Web, visit http://www.gromacs.org/mailman/listinfo/gmx-users or, via email, send a message with subject or body 'help' to gmx-users-requ...@gromacs.org You can reach the person managing the list at gmx-users-ow...@gromacs.org When replying, please edit your Subject line so it is more specific than "Re: Contents of gmx-users digest..." Today's Topics: 1. Re: gmx-users Digest, Vol 58, Issue 2 (Ms. Aswathy S) 2. RE: Re: gmx-users Digest, Vol 58, Issue 2 (Mohammed Kamal) 3. Re: COM motion removal (Mark Abraham) 4. infinite polymer crystals at gromacs 4.x.x (Claus Valka) ------ Message: 1 Date: Sun, 1 Feb 2009 16:49:17 +0530 (IST) From: "Ms. Aswathy S" Subject: [gmx-users] Re: gmx-users Digest, Vol 58, Issue 2 To: gmx-users@gromacs.org Message-ID: <7604642.142011233487157801.javamail.r...@durga.amrita.ac.in> Content-Type: text/plain; charset=utf-8 Dear Mohammed, Thanks for your reply. The .ITP file from the PRODRG server has saved as drg.itp and added "#include "drg.itp"" line in the topology file. still getting the same error. Where should I save the drg.itp file in the present working directory or share/top directory? Thanks, Aswathy Dept. Biotechnology Ext. 3108 - Original Message - From: gmx-users-requ...@gromacs.org To: gmx-users@gromacs.org Sent: Sunday, February 1, 2009 4:30:04 PM GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi Subject: gmx-users Digest, Vol 58, Issue 2 Send gmx-users mailing list submissions to gmx-users@gromacs.org To subscribe or unsubscribe via the World Wide Web, visit http://www.gromacs.org/mailman/listinfo/gmx-users or, via email, send a message with subject or body 'help' to gmx-users-requ...@gromacs.org You can reach the person managing the list at gmx-users-ow...@gromacs.org When replying, please edit your Subject line so it is more specific than "Re: Contents of gmx-users digest..." Today's Topics: 1. RE: IN4 molecule type error (Mohammed Kamal) -- Message: 1 Date: Sun, 1 Feb 2009 21:11:11 +1100 From: Mohammed Kamal Subject: RE: [gmx-users] IN4 molecule type error To: Gromacs Message-ID: Content-Type: text/plain; charset="iso-8859-1" You have to include the .itp file that you have obtained from PRODRG in the topology file. Be sure that you have changed the extension of the .itp file that you have obtained from the PRODRG server from .ITP to .itp!! Mohammed > Date: Fri, 30 Jan 2009 20:57:28 +0530 > From: aswat...@amritapuri.amrita.edu > To: gmx-users@gromacs.org > Subject: [gmx-users] IN4 molecule type error > > Dear Gromacs users, > > I am a new user of gromacs. I was trying the Enzyme- Drug complex tutorial > for a test run and i have ended up with following error. Please try to help me > > > creating statusfile for 1 node... > > Back Off! I just backed up mdout.mdp to ./#mdout.mdp.90# > checking input for internal consistency... > calling /usr/bin/cpp... > TEST1/trp.top:12:9: error: #include expects "FILENAME" or > cpp exit code: 256 > Tried to execute: '/usr/bin/cpp -I/usr/local
[gmx-users] Re: IN4 molecule type error
Sorry for the mistake.. It worked well!!! Thank you... Aswathy Dept. Biotechnology Ext. 3108 - Original Message - From: gmx-users-requ...@gromacs.org To: gmx-users@gromacs.org Sent: Tuesday, February 3, 2009 1:47:57 PM GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi Subject: gmx-users Digest, Vol 58, Issue 16 Send gmx-users mailing list submissions to gmx-users@gromacs.org To subscribe or unsubscribe via the World Wide Web, visit http://www.gromacs.org/mailman/listinfo/gmx-users or, via email, send a message with subject or body 'help' to gmx-users-requ...@gromacs.org You can reach the person managing the list at gmx-users-ow...@gromacs.org When replying, please edit your Subject line so it is more specific than "Re: Contents of gmx-users digest..." Today's Topics: 1. Re: Re: IN4 molecule type error (Justin A. Lemkul) 2. Re: Re: IN4 molecule type error (Mark Abraham) 3. Re: Re: IN4 molecule type error (Mark Abraham) 4. free energy decomposition (friendli) -- Message: 1 Date: Mon, 02 Feb 2009 22:13:23 -0500 From: "Justin A. Lemkul" Subject: Re: [gmx-users] Re: IN4 molecule type error To: Discussion list for GROMACS users Message-ID: <4987b653.8090...@vt.edu> Content-Type: text/plain; charset=UTF-8; format=flowed Ms. Aswathy S wrote: > Hi, > > I have added the #include "drg.itp" statement under the title, ; Include > forcefield parameters in the .top file. Thr drg.itp is saved in the current > directory. > This is the incorrect order. You've inserted the drg.itp moleculetype information before your protein, then called the protein before IN4 in the [ molecules ] section. Order is important. Include the moleculetypes in the order that they appear in the structure file (.pdb or .gro). See a few comments embedded below. > Still showing the sanme error as previous. > > including a part of the top file.Please check this. > > ; This is your topology file > ; TRYPSIN > ; > ; Include forcefield parameters > #include "ffgmx.itp" > #include�� "drg.itp"�� > I don't know if this is just strange behavior from my email client, but if you've got these hidden characters within this line of text, it will not be interpreted correctly. Make sure you are using a plain text editor, like vi or emacs, to edit your topology file. > [ moleculetype ] > ; Namenrexcl > Protein_A 3 > > > At the end, > > ; Include Position restraint file > #ifdef POSRES > #include "posre.itp" > #endif > * This is where you should #include "drg.itp" * The position restraint information relates to the protein moleculetype definition, therefore ending the information for this particular molecule. I suggest a thorough read of Chapter 5 to become more familiar with the Gromacs topology structure. I believe this information is explained in John Kerrigan's tutorial, as well. -Justin > ; Include water topology > #include "spce.itp" > > #ifdef POSRES_WATER > ; Position restraint for each water oxygen > [ position_restraints ] > ; i funct fcxfcyfcz >11 1000 1000 1000 > #endif > > ; Include generic topology for ions > #include "ions.itp" > > [ system ] > ; Name > TRYPSIN in water > > [ molecules ] > ; Compound#mols > Protein_A 1 > IN4 1 > SOL 8902 > ___ > > Thanks, > Aswathy > Dept. Biotechnology > Ext. 3108 > > - Original Message - > From: gmx-users-requ...@gromacs.org > To: gmx-users@gromacs.org > Sent: Sunday, February 1, 2009 9:28:44 PM GMT +05:30 Chennai, Kolkata, > Mumbai, New Delhi > Subject: gmx-users Digest, Vol 58, Issue 3 > > Send gmx-users mailing list submissions to > gmx-users@gromacs.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.gromacs.org/mailman/listinfo/gmx-users > or, via email, send a message with subject or body 'help' to > gmx-users-requ...@gromacs.org > > You can reach the person managing the list at > gmx-users-ow...@gromacs.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of gmx-users digest..." > > > Today's Topics: > >1. Re: gmx-users Digest, Vol 58, Issue 2 (Ms. Aswathy S) >2. RE: Re: gmx-users Digest, Vol 58, Issue 2 (Mohammed Kamal) >
[gmx-users] Ligand is moving far away after energy minimization
Dear Gromacs users, I am doing the MD of protein ligand complex. When I did the energy minimization of this complex, in the result , the ligand molceule is moving far away from the protein. What could be the possible reason? can anyone tell me how can i overcome this? Thanks in advance. Aswathy Amrita School of biotechnology Dept. Biotechnology Ext. 3108 ___ 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: Ligand is moving far away after energy minimization
Ms. Aswathy S wrote: > Dear Gromacs users, > > I am doing the MD of protein ligand complex. When I did the energy > minimization of this complex, in the result , the ligand molceule is moving > far away from the protein. > > What could be the possible reason? can anyone tell me how can i overcome this? > Two possibilities come to my mind. 1. The parameters of the ligand are inappropriate, causing the ligand to be ejected from the active site. This is unlikely in a simple EM procedure, and probably would cause lots of LINCS or "blowing up" warnings. 2. More likely: Your protein is positioned near a box edge and the ligand is crossing periodic boundaries. Consider how you set up the box and read about PBC: http://wiki.gromacs.org/index.php/Periodic_Boundary_Conditions -Justin Here I dint get any error message as you mentoined in th first possiblity.Then about the seocnd suggestion, only two options provided to in the manual. pbd : no and pbc: xyz. I havn;t found any change in my problrm. can you rxplain a liitle bit more. waiting for you reply > Thanks in advance. > > Aswathy > Amrita School of biotechnology > Dept. Biotechnology > Ext. 3108 > ___ > gmx-users mailing listgmx-users at 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-request at gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Justin A. Lemkul Graduate Research Assistant 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://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] Fwd: Segmentation fault while running gromacs 4.0.4
Dept. Biotechnology
Ext. 3108
- Forwarded Message -
From: "Ms. Aswathy S"
To: gmx-users@gromacs.org
Sent: Tuesday, June 2, 2009 11:54:56 AM GMT +05:30 Chennai, Kolkata, Mumbai,
New Delhi
Subject: Segmentation fault while running gromacs 4.0.4
Hi,
I am working in GROMACS 4.0.4 and trying to do a receptor -ligand simulation.
But when I run the grommp for equilibration of about 30 ps, it shows
Segmentaion Fault. I din't get any idea that what type of error it causing from
the log file. When i run the free command it has a free space of 33 MB. Is that
could be the reason?. But I already read that gromacs doesnot consume that much
memory(10-20Mb). If so tell me what could be the possibilities. attaching the
mdp file and log file
I will explain all the steps i have did,
1. The protein and ligand i minimized in vaccum.
2. Then added water and again minimized the whole system (During both 1 & 2
minimization, "Steepest Descents converged to machine precision "in early steps
)
3. I used the otput file from the above result for equilibration steps(is that
the reason??!!!)
then i faced the segmentatuion fault. Please help me
thanks in advance
Dept. Biotechnology
Ext. 3108
Log file opened on Mon Jun 1 11:53:59 2009
Host: localhost.localdomain pid: 8316 nodeid: 0 nnodes: 1
The Gromacs distribution was built Wed May 13 12:15:31 IST 2009 by
r...@localhost.localdomain (Linux 2.6.18-92.el5xen i686)
:-) G R O M A C S (-:
Groningen Machine for Chemical Simulation
:-) VERSION 4.0.4 (-:
Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2008, The GROMACS development team,
check out http://www.gromacs.org for more information.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
:-) mdrun (-:
PLEASE READ AND CITE THE FOLLOWING REFERENCE
B. Hess and C. Kutzner and D. van der Spoel and E. Lindahl
GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable
molecular simulation
J. Chem. Theory Comput. 4 (2008) pp. 435-447
--- Thank You ---
PLEASE READ AND CITE THE FOLLOWING REFERENCE
D. van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark and H. J. C.
Berendsen
GROMACS: Fast, Flexible and Free
J. Comp. Chem. 26 (2005) pp. 1701-1719
--- Thank You ---
PLEASE READ AND CITE THE FOLLOWING REFERENCE
E. Lindahl and B. Hess and D. van der Spoel
GROMACS 3.0: A package for molecular simulation and trajectory analysis
J. Mol. Mod. 7 (2001) pp. 306-317
--- Thank You ---
PLEASE READ AND CITE THE FOLLOWING REFERENCE
H. J. C. Berendsen, D. van der Spoel and R. van Drunen
GROMACS: A message-passing parallel molecular dynamics implementation
Comp. Phys. Comm. 91 (1995) pp. 43-56
--- Thank You ---
Input Parameters:
integrator = md
nsteps = 5000
init_step= 0
ns_type = Grid
nstlist = 10
ndelta = 2
nstcomm = 1
comm_mode= Linear
nstlog = 100
nstxout = 250
nstvout = 1000
nstfout = 0
nstenergy= 10
nstxtcout= 100
init_t = 0
delta_t = 0.002
xtcprec = 1000
nkx = 60
nky = 60
nkz = 60
pme_order= 4
ewald_rtol = 1e-05
ewald_geometry = 0
epsilon_surface = 0
optimize_fft = FALSE
ePBC = xyz
bPeriodicMols= FALSE
bContinuation= FALSE
bShakeSOR= FALSE
etc = Berendsen
epc = Berendsen
epctype = Isotropic
tau_p= 0.5
ref_p (3x3):
ref_p[0]={ 1.0e+00, 0.0e+00, 0.0e+00}
ref_p[1]={ 0.0e+00, 1.0e+00, 0.0e+00}
ref_p[2]={ 0.0e+00, 0.0e+00, 1.0e+00}
compress (3x3):
compress[0]={ 4.5e-05, 0.0e+00, 0.0e+00}
compress[1]={ 0.0e+00, 4.5e-05, 0.0e+00}
compress[2]={ 0.0e+00, 0.0e+00, 4.5e-05}
refcoord_scaling = No
posres_com (3):
posres_com[0]= 0.0e+00
posres_com[1]= 0.0e+00
posres_com[2]= 0.0e+00
posres_comB (3):
