RE: [gmx-users] Transition difficulties: version 3.3.3 to 4.0.3 regarding pull_geometry=distance
Hi, You can mail the system to me. Please include all the details required to run the system and the different results you get with the exact Gromacs version numbers. Berk Date: Wed, 28 Jan 2009 00:52:06 -0500 From: fied...@umich.edu To: gmx-users@gromacs.org Subject: Re: [gmx-users] Transition difficulties: version 3.3.3 to 4.0.3 regarding pull_geometry=distance Hi, The permeants in my bilayer system are improperly pulled in calculations using all versions of Gromacs 4.0.x including the VERSION 4.0.99_development_20090120. Since, due to restrictions, I can not provide the topology file for my system to bugzilla, I constructed a similar prototypical system using Prof. Tieleman's POPC bilayer coordinates and field parameters. A buckyball permenat doped in the center of this system did indeed react similarly in a 4.0.3 calculation with an improper pull away from the equilibrated 3.3.1 constraint force coordinates. It was heartening to see that this problem was fixed for that system, by using VERSION 4.0.99_development_20090120. Unfortunately, again the problem remained for my actual system, even with use of the newest version of code. Since the cylinder option is now operational, I have a viable work-around for this problem. I am quite appreciative of the attention that this issue has received. If there is continued interest, and a willingness for an engineer to receive the topology file in a less public forum than bugzilla, I believe we could proceed with the debugging process. Thank you, Steve Fiedler Berk Hess wrote: Hi, Just to be sure, the pull code is producing the correct results now? The only problems should be in several analysis tools. The analysis tools have been written only with analysis of molecules or parts of molecules in mind. When you want to analyze groups that cover two molecules or more there will be pbc problems. These are not simple to fix. If the distances between all the atoms in the group are less than half a box length there is a unique COM. The procedure should be similar to what trjconv -pbc cluster does. I can try to implement this for g_traj and g_dist. Are there other tools that cause problems? Berk Date: Mon, 26 Jan 2009 17:46:26 -0500 From: fied...@umich.edu To: gmx-users@gromacs.org Subject: Re: [gmx-users] Transition difficulties: version 3.3.3 to 4.0.3 regarding pull_geometry=distance Hi Chris, Your suggestions were helpful. Due to the nature of this problem, there were limitations in the application of the sequence of steps that you recommended. Specifically, the difference in the equilibrated structure from version 3.3.x to the calculated reference center of mass from version 4.0.x causes an unreasonable jump with constraint force calculation. Resultant bad contacts prohibit generation of a pull output file. More generally though, I believe I understand your broader point: the sensitive nature of the periodic box with respect to the pull code and possible discrepancies in the pbc treatment by various utilities, may cause confusion with the diagnostic process. The test bilayer system I created however, centered distantly from the x and y box edges, may effectively remove this set of concerns. For example, this configuration is relatively unchanged upon recentering, however it is still susceptible to the problem that is the subject of this discussion. If I can reproduce this phenomenon with a publicly available topology file, I can provide the necessary input files for inspection. Thank you again, Steve Fiedler chris.ne...@utoronto.ca wrote: Hi Steve, what I intended to suggest was actually something different (and much easier). The idea is not that you need some special system to be able to utilize the pull code, but that the pull code is correct whereas the g_dist and g_traj programs are not as good at treating pbc in the way that one desires. I suggest the following. 1. Take your original system and run the pull code for a very short simulation. Use the last line of the output to calculate the relevant displacement 2. Now use trjconv -b -e to get the last frame of the .xtc that resulted from that short MD run as a .gro file, call it final.gro. I suspect that your groups are not entirely in the same simulation box in final.gro. 3. Now make a new .ndx file from that .gro and give it a single residue that is near your binding pocket, call it R_1 4. Now apply trjconv -center -pbc mol -ur compact while selecting R_1 for centering, call the new .gro file final_center.gro 5. Visualize final_center.gro and ensure that all of your relevant atoms are in the same image in the way that puts the minimum distance between them along a path
RE: [gmx-users] Transition difficulties: version 3.3.3 to 4.0.3 regarding pull_geometry=distance
Hi, This issue has been resolved. It was indeed a problem of a pull group consisting of multiple molecules. In this case the choice of the pull_pbcatom mdp parameter was critical. If you do not set this, it takes the numerically middle atom of the group. In this case that was an atom in a lipid head group. The distance of this reference head group atom to the head groups on the other side of the bilayer was shorter through pbc and the solvent than through the bilayer. Setting pull_pbcatom by hand to a tail end atom resolved the issue. Berk From: g...@hotmail.com To: gmx-users@gromacs.org Subject: RE: [gmx-users] Transition difficulties: version 3.3.3 to 4.0.3 regarding pull_geometry=distance Date: Wed, 28 Jan 2009 10:45:33 +0100 Hi, You can mail the system to me. Please include all the details required to run the system and the different results you get with the exact Gromacs version numbers. Berk Date: Wed, 28 Jan 2009 00:52:06 -0500 From: fied...@umich.edu To: gmx-users@gromacs.org Subject: Re: [gmx-users] Transition difficulties: version 3.3.3 to 4.0.3 regarding pull_geometry=distance Hi, The permeants in my bilayer system are improperly pulled in calculations using all versions of Gromacs 4.0.x including the VERSION 4.0.99_development_20090120. Since, due to restrictions, I can not provide the topology file for my system to bugzilla, I constructed a similar prototypical system using Prof. Tieleman's POPC bilayer coordinates and field parameters. A buckyball permenat doped in the center of this system did indeed react similarly in a 4.0.3 calculation with an improper pull away from the equilibrated 3.3.1 constraint force coordinates. It was heartening to see that this problem was fixed for that system, by using VERSION 4.0.99_development_20090120. Unfortunately, again the problem remained for my actual system, even with use of the newest version of code. Since the cylinder option is now operational, I have a viable work-around for this problem. I am quite appreciative of the attention that this issue has received. If there is continued interest, and a willingness for an engineer to receive the topology file in a less public forum than bugzilla, I believe we could proceed with the debugging process. Thank you, Steve Fiedler Berk Hess wrote: Hi, Just to be sure, the pull code is producing the correct results now? The only problems should be in several analysis tools. The analysis tools have been written only with analysis of molecules or parts of molecules in mind. When you want to analyze groups that cover two molecules or more there will be pbc problems. These are not simple to fix. If the distances between all the atoms in the group are less than half a box length there is a unique COM. The procedure should be similar to what trjconv -pbc cluster does. I can try to implement this for g_traj and g_dist. Are there other tools that cause problems? Berk Date: Mon, 26 Jan 2009 17:46:26 -0500 From: fied...@umich.edu To: gmx-users@gromacs.org Subject: Re: [gmx-users] Transition difficulties: version 3.3.3 to 4.0.3 regarding pull_geometry=distance Hi Chris, Your suggestions were helpful. Due to the nature of this problem, there were limitations in the application of the sequence of steps that you recommended. Specifically, the difference in the equilibrated structure from version 3.3.x to the calculated reference center of mass from version 4.0.x causes an unreasonable jump with constraint force calculation. Resultant bad contacts prohibit generation of a pull output file. More generally though, I believe I understand your broader point: the sensitive nature of the periodic box with respect to the pull code and possible discrepancies in the pbc treatment by various utilities, may cause confusion with the diagnostic process. The test bilayer system I created however, centered distantly from the x and y box edges, may effectively remove this set of concerns. For example, this configuration is relatively unchanged upon recentering, however it is still susceptible to the problem that is the subject of this discussion. If I can reproduce this phenomenon with a publicly available topology file, I can provide the necessary input files for inspection. Thank you again, Steve Fiedler chris.ne...@utoronto.ca wrote: Hi Steve, what I intended to suggest was actually something different (and much easier). The idea is not that you need some special system to be able to utilize the pull code, but that the pull code is correct whereas the g_dist and g_traj programs are not as good at treating pbc in the way that one desires. I suggest the following. 1. Take your original system and run the pull code for a very short simulation. Use
RE: [gmx-users] Transition difficulties: version 3.3.3 to 4.0.3 regarding pull_geometry=distance
Hi, Just to be sure, the pull code is producing the correct results now? The only problems should be in several analysis tools. The analysis tools have been written only with analysis of molecules or parts of molecules in mind. When you want to analyze groups that cover two molecules or more there will be pbc problems. These are not simple to fix. If the distances between all the atoms in the group are less than half a box length there is a unique COM. The procedure should be similar to what trjconv -pbc cluster does. I can try to implement this for g_traj and g_dist. Are there other tools that cause problems? Berk Date: Mon, 26 Jan 2009 17:46:26 -0500 From: fied...@umich.edu To: gmx-users@gromacs.org Subject: Re: [gmx-users] Transition difficulties: version 3.3.3 to4.0.3 regarding pull_geometry=distance Hi Chris, Your suggestions were helpful. Due to the nature of this problem, there were limitations in the application of the sequence of steps that you recommended. Specifically, the difference in the equilibrated structure from version 3.3.x to the calculated reference center of mass from version 4.0.x causes an unreasonable jump with constraint force calculation. Resultant bad contacts prohibit generation of a pull output file. More generally though, I believe I understand your broader point: the sensitive nature of the periodic box with respect to the pull code and possible discrepancies in the pbc treatment by various utilities, may cause confusion with the diagnostic process. The test bilayer system I created however, centered distantly from the x and y box edges, may effectively remove this set of concerns. For example, this configuration is relatively unchanged upon recentering, however it is still susceptible to the problem that is the subject of this discussion. If I can reproduce this phenomenon with a publicly available topology file, I can provide the necessary input files for inspection. Thank you again, Steve Fiedler chris.ne...@utoronto.ca wrote: Hi Steve, what I intended to suggest was actually something different (and much easier). The idea is not that you need some special system to be able to utilize the pull code, but that the pull code is correct whereas the g_dist and g_traj programs are not as good at treating pbc in the way that one desires. I suggest the following. 1. Take your original system and run the pull code for a very short simulation. Use the last line of the output to calculate the relevant displacement 2. Now use trjconv -b -e to get the last frame of the .xtc that resulted from that short MD run as a .gro file, call it final.gro. I suspect that your groups are not entirely in the same simulation box in final.gro. 3. Now make a new .ndx file from that .gro and give it a single residue that is near your binding pocket, call it R_1 4. Now apply trjconv -center -pbc mol -ur compact while selecting R_1 for centering, call the new .gro file final_center.gro 5. Visualize final_center.gro and ensure that all of your relevant atoms are in the same image in the way that puts the minimum distance between them along a path that is entirely contained within the unit cell. If not, go back to step 3 and try making a group R_2, etc. until this process works. NOTE: you might think that giving trjconv -center the relevant groups that you use for pulling will be a good idea here, but it is not. The problem there is that the atoms may be centered by placing half on the left boundary and half on the right boundary. I find using one logically selected residue or atom is the best method here. 6. Assuming that you got what you wanted in step 5, now run g_traj and g_dist on final_center.gro. In my case, I found that g_traj and g_dist give the same answer as the pull code output when I am using final_center.gro, but not always when I am using final.gro. *** I always laugh when these problems arise because, in an important sense, the protein *did* jump out of the simulation box... at least as far as g_traj and g_dist are concerned. This, we must hope, is correctly treated in the pull code even though it is incorrectly (or at least unintuitively) treated by g_traj and g_dist. Chris. -- original message -- Hi, Thank you Berk and Chris for the suggestions. To address the possibility that this issue is related to periodic boundaries, I used two approaches: 1. The pull group of interest (permeant) was centered in the x-y plane of the box using Chris' approach. I then used the genconf utility to replicate my lipid box to a 9x9 grid in the x-y plane and removed all but the center box. This generated the coordinates for a bilayer system with all lipid molecules inside a box and intact. The discrepancy between the grompp (version 4.0.3) output and distances
Re: [gmx-users] Transition difficulties: version 3.3.3 to 4.0.3 regarding pull_geometry=distance
Dear Berk, I think that g_clustsize has a similar problem. IIRC I fixed it in a similar way on my own copy. There are probably other tools that will suffer from this as well, but for g_clustsize it's important because it may deal with such groups. Same goes for trjconv, e.g., for a protein and ligand. Ran. Berk Hess wrote: Hi, Just to be sure, the pull code is producing the correct results now? The only problems should be in several analysis tools. The analysis tools have been written only with analysis of molecules or parts of molecules in mind. When you want to analyze groups that cover two molecules or more there will be pbc problems. These are not simple to fix. If the distances between all the atoms in the group are less than half a box length there is a unique COM. The procedure should be similar to what trjconv -pbc cluster does. I can try to implement this for g_traj and g_dist. Are there other tools that cause problems? Berk Date: Mon, 26 Jan 2009 17:46:26 -0500 From: fied...@umich.edu To: gmx-users@gromacs.org Subject: Re: [gmx-users] Transition difficulties: version 3.3.3 to 4.0.3 regarding pull_geometry=distance Hi Chris, Your suggestions were helpful. Due to the nature of this problem, there were limitations in the application of the sequence of steps that you recommended. Specifically, the difference in the equilibrated structure from version 3.3.x to the calculated reference center of mass from version 4.0.x causes an unreasonable jump with constraint force calculation. Resultant bad contacts prohibit generation of a pull output file. More generally though, I believe I understand your broader point: the sensitive nature of the periodic box with respect to the pull code and possible discrepancies in the pbc treatment by various utilities, may cause confusion with the diagnostic process. The test bilayer system I created however, centered distantly from the x and y box edges, may effectively remove this set of concerns. For example, this configuration is relatively unchanged upon recentering, however it is still susceptible to the problem that is the subject of this discussion. If I can reproduce this phenomenon with a publicly available topology file, I can provide the necessary input files for inspection. Thank you again, Steve Fiedler chris.ne...@utoronto.ca wrote: Hi Steve, what I intended to suggest was actually something different (and much easier). The idea is not that you need some special system to be able to utilize the pull code, but that the pull code is correct whereas the g_dist and g_traj programs are not as good at treating pbc in the way that one desires. I suggest the following. 1. Take your original system and run the pull code for a very short simulation. Use the last line of the output to calculate the relevant displacement 2. Now use trjconv -b -e to get the last frame of the .xtc that resulted from that short MD run as a .gro file, call it final.gro. I suspect that your groups are not entirely in the same simulation box in final.gro. 3. Now make a new .ndx file from that .gro and give it a single residue that is near your binding pocket, call it R_1 4. Now apply trjconv -center -pbc mol -ur compact while selecting R_1 for centering, call the new .gro file final_center.gro 5. Visualize final_center.gro and ensure that all of your relevant atoms are in the same image in the way that puts the minimum distance between them along a path that is entirely contained within the unit cell. If not, go back to step 3 and try making a group R_2, etc. until this process works. NOTE: you might think that giving trjconv -center the relevant groups that you use for pulling will be a good idea here, but it is not. The problem there is that the atoms may be centered by placing half on the left boundary and half on the right boundary. I find using one logically selected residue or atom is the best method here. 6. Assuming that you got what you wanted in step 5, now run g_traj and g_dist on final_center.gro. In my case, I found that g_traj and g_dist give the same answer as the pull code output when I am using final_center.gro, but not always when I am using final.gro. *** I always laugh when these problems arise because, in an important sense, the protein *did* jump out of the simulation box... at least as far as g_traj and g_dist are concerned. This, we must hope, is correctly treated in the pull code even though it is incorrectly (or at least unintuitively) treated by g_traj and g_dist. Chris. -- original message -- Hi, Thank you Berk and Chris for the suggestions. To address the possibility that this issue is related to periodic boundaries, I used two approaches: 1. The pull group of interest (permeant) was centered
RE: [gmx-users] Transition difficulties: version 3.3.3 to 4.0.3 regarding pull_geometry=distance
Hi, I think g_clustsize requires a different algorithm. Here you don't know a priori what the group is. I guess things are easier here, since you always cluster (parts of) molecules. Or am I wrong? I am not familiar with this program. If there are problems, please file a bugzilla. Berk Date: Tue, 27 Jan 2009 09:58:32 +0100 From: r.fried...@bioc.uzh.ch To: gmx-users@gromacs.org Subject: Re: [gmx-users] Transition difficulties: version 3.3.3 to 4.0.3 regarding pull_geometry=distance Dear Berk, I think that g_clustsize has a similar problem. IIRC I fixed it in a similar way on my own copy. There are probably other tools that will suffer from this as well, but for g_clustsize it's important because it may deal with such groups. Same goes for trjconv, e.g., for a protein and ligand. Ran. Berk Hess wrote: Hi, Just to be sure, the pull code is producing the correct results now? The only problems should be in several analysis tools. The analysis tools have been written only with analysis of molecules or parts of molecules in mind. When you want to analyze groups that cover two molecules or more there will be pbc problems. These are not simple to fix. If the distances between all the atoms in the group are less than half a box length there is a unique COM. The procedure should be similar to what trjconv -pbc cluster does. I can try to implement this for g_traj and g_dist. Are there other tools that cause problems? Berk Date: Mon, 26 Jan 2009 17:46:26 -0500 From: fied...@umich.edu To: gmx-users@gromacs.org Subject: Re: [gmx-users] Transition difficulties: version 3.3.3 to 4.0.3 regarding pull_geometry=distance Hi Chris, Your suggestions were helpful. Due to the nature of this problem, there were limitations in the application of the sequence of steps that you recommended. Specifically, the difference in the equilibrated structure from version 3.3.x to the calculated reference center of mass from version 4.0.x causes an unreasonable jump with constraint force calculation. Resultant bad contacts prohibit generation of a pull output file. More generally though, I believe I understand your broader point: the sensitive nature of the periodic box with respect to the pull code and possible discrepancies in the pbc treatment by various utilities, may cause confusion with the diagnostic process. The test bilayer system I created however, centered distantly from the x and y box edges, may effectively remove this set of concerns. For example, this configuration is relatively unchanged upon recentering, however it is still susceptible to the problem that is the subject of this discussion. If I can reproduce this phenomenon with a publicly available topology file, I can provide the necessary input files for inspection. Thank you again, Steve Fiedler chris.ne...@utoronto.ca wrote: Hi Steve, what I intended to suggest was actually something different (and much easier). The idea is not that you need some special system to be able to utilize the pull code, but that the pull code is correct whereas the g_dist and g_traj programs are not as good at treating pbc in the way that one desires. I suggest the following. 1. Take your original system and run the pull code for a very short simulation. Use the last line of the output to calculate the relevant displacement 2. Now use trjconv -b -e to get the last frame of the .xtc that resulted from that short MD run as a .gro file, call it final.gro. I suspect that your groups are not entirely in the same simulation box in final.gro. 3. Now make a new .ndx file from that .gro and give it a single residue that is near your binding pocket, call it R_1 4. Now apply trjconv -center -pbc mol -ur compact while selecting R_1 for centering, call the new .gro file final_center.gro 5. Visualize final_center.gro and ensure that all of your relevant atoms are in the same image in the way that puts the minimum distance between them along a path that is entirely contained within the unit cell. If not, go back to step 3 and try making a group R_2, etc. until this process works. NOTE: you might think that giving trjconv -center the relevant groups that you use for pulling will be a good idea here, but it is not. The problem there is that the atoms may be centered by placing half on the left boundary and half on the right boundary. I find using one logically selected residue or atom is the best method here. 6. Assuming that you got what you wanted in step 5, now run g_traj and g_dist on final_center.gro. In my case, I found that g_traj and g_dist give the same answer as the pull code output when I am using final_center.gro, but not always when I am using final.gro. *** I always laugh when
Re: [gmx-users] Transition difficulties: version 3.3.3 to 4.0.3 regarding pull_geometry=distance
Hi, The permeants in my bilayer system are improperly pulled in calculations using all versions of Gromacs 4.0.x including the VERSION 4.0.99_development_20090120. Since, due to restrictions, I can not provide the topology file for my system to bugzilla, I constructed a similar prototypical system using Prof. Tieleman's POPC bilayer coordinates and field parameters. A buckyball permenat doped in the center of this system did indeed react similarly in a 4.0.3 calculation with an improper pull away from the equilibrated 3.3.1 constraint force coordinates. It was heartening to see that this problem was fixed for that system, by using VERSION 4.0.99_development_20090120. Unfortunately, again the problem remained for my actual system, even with use of the newest version of code. Since the cylinder option is now operational, I have a viable work-around for this problem. I am quite appreciative of the attention that this issue has received. If there is continued interest, and a willingness for an engineer to receive the topology file in a less public forum than bugzilla, I believe we could proceed with the debugging process. Thank you, Steve Fiedler Berk Hess wrote: Hi, Just to be sure, the pull code is producing the correct results now? The only problems should be in several analysis tools. The analysis tools have been written only with analysis of molecules or parts of molecules in mind. When you want to analyze groups that cover two molecules or more there will be pbc problems. These are not simple to fix. If the distances between all the atoms in the group are less than half a box length there is a unique COM. The procedure should be similar to what trjconv -pbc cluster does. I can try to implement this for g_traj and g_dist. Are there other tools that cause problems? Berk Date: Mon, 26 Jan 2009 17:46:26 -0500 From: fied...@umich.edu To: gmx-users@gromacs.org Subject: Re: [gmx-users] Transition difficulties: version 3.3.3 to 4.0.3 regarding pull_geometry=distance Hi Chris, Your suggestions were helpful. Due to the nature of this problem, there were limitations in the application of the sequence of steps that you recommended. Specifically, the difference in the equilibrated structure from version 3.3.x to the calculated reference center of mass from version 4.0.x causes an unreasonable jump with constraint force calculation. Resultant bad contacts prohibit generation of a pull output file. More generally though, I believe I understand your broader point: the sensitive nature of the periodic box with respect to the pull code and possible discrepancies in the pbc treatment by various utilities, may cause confusion with the diagnostic process. The test bilayer system I created however, centered distantly from the x and y box edges, may effectively remove this set of concerns. For example, this configuration is relatively unchanged upon recentering, however it is still susceptible to the problem that is the subject of this discussion. If I can reproduce this phenomenon with a publicly available topology file, I can provide the necessary input files for inspection. Thank you again, Steve Fiedler chris.ne...@utoronto.ca wrote: Hi Steve, what I intended to suggest was actually something different (and much easier). The idea is not that you need some special system to be able to utilize the pull code, but that the pull code is correct whereas the g_dist and g_traj programs are not as good at treating pbc in the way that one desires. I suggest the following. 1. Take your original system and run the pull code for a very short simulation. Use the last line of the output to calculate the relevant displacement 2. Now use trjconv -b -e to get the last frame of the .xtc that resulted from that short MD run as a .gro file, call it final.gro. I suspect that your groups are not entirely in the same simulation box in final.gro. 3. Now make a new .ndx file from that .gro and give it a single residue that is near your binding pocket, call it R_1 4. Now apply trjconv -center -pbc mol -ur compact while selecting R_1 for centering, call the new .gro file final_center.gro 5. Visualize final_center.gro and ensure that all of your relevant atoms are in the same image in the way that puts the minimum distance between them along a path that is entirely contained within the unit cell. If not, go back to step 3 and try making a group R_2, etc. until this process works. NOTE: you might think that giving trjconv -center the relevant groups that you use for pulling will be a good idea here, but it is not. The problem there is that the atoms may be centered by placing half on the left boundary and half on the right boundary. I find using one logically selected residue or atom is the best method here. 6. Assuming that you got what you wanted in step 5, now run g_traj and g_dist
[gmx-users] Transition difficulties: version 3.3.3 to 4.0.3 regarding pull_geometry=distance
Hi Steve, I also use the pull code and would be very interested to more fully understand the problem that you are experiencing. However, I don't generally modify any code myself, and therefore have no use for your private system. What I would be eager to receive is your POPC-buckyball system with a small instruction on how I might detect the difference between 4.0.3 and 4.0.99 behaviour. chris.neale |at| utoronto.ca Chris. -- original message -- Hi, The permeants in my bilayer system are improperly pulled in calculations using all versions of Gromacs 4.0.x including the VERSION 4.0.99_development_20090120. Since, due to restrictions, I can not provide the topology file for my system to bugzilla, I constructed a similar prototypical system using Prof. Tieleman's POPC bilayer coordinates and field parameters. A buckyball permenat doped in the center of this system did indeed react similarly in a 4.0.3 calculation with an improper pull away from the equilibrated 3.3.1 constraint force coordinates. It was heartening to see that this problem was fixed for that system, by using VERSION 4.0.99_development_20090120. Unfortunately, again the problem remained for my actual system, even with use of the newest version of code. Since the cylinder option is now operational, I have a viable work-around for this problem. I am quite appreciative of the attention that this issue has received. If there is continued interest, and a willingness for an engineer to receive the topology file in a less public forum than bugzilla, I believe we could proceed with the debugging process. Thank you, Steve Fiedler ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] Transition difficulties: version 3.3.3 to 4.0.3 regarding pull_geometry=distance
Hi,
Strange, I think I have really fixed all problems now.
All test systems work fine for me.
Can you file a bugzilla entry?
Please include all the files needed to run grompp
as well as the correct pull distance and the pull distance you obtained.
Berk
Date: Sun, 25 Jan 2009 23:45:29 -0500
From: fied...@umich.edu
To: gmx-users@gromacs.org
Subject: Re: [gmx-users] Transition difficulties: version 3.3.3 to
4.0.3 regarding pull_geometry=distance
Hi,
I rebuilt the code using both sets of Berk's corrections. On an
isolated bilayer system with no periodic boundaries in the x-y plane
prepared in the manner previously explained, the recompiled grompp
output yielded no improvement in the discrepancies of the position of a
buckyball permeant. By visual inspection, it appears that the 4.0.x
versions still attempt to distort the position of the permeant
significant upward from the bilayer center, i.e., the center of mass of
the reference group. Interestingly, the 3.3.x and 4.0.x version
identically treated a test bilayer system constructed with a single
dummy particle permeant.
I appreciate the help of Berk, and Chris' detailed suggestions with this
interesting problem.
Sincerely,
Steve Fiedler
Berk Hess wrote:
Hi,
I just found out that I introduced a bug in 4.0.3, which could cause
the pull code to crash or give wrong results when running single
processor.
In parallel it is correct.
I committed fixed for 4.0.4.
If you run in parallel things should be correct,
or change in src/kernel/md.c:
if (ir-pull) {
dd_make_local_pull_groups(NULL,ir-pull,mdatoms);
to
if (ir-pull PAR(cr)) {
dd_make_local_pull_groups(NULL,ir-pull,mdatoms);
Berk
Date: Fri, 23 Jan 2009 12:14:43 -0500
From: fied...@umich.edu
To: gmx-users@gromacs.org
Subject: Re: [gmx-users] Transition difficulties: version 3.3.3 to
4.0.3 regarding pull_geometry=distance
Hi,
Thank you Berk and Chris for the suggestions.
To address the possibility that this issue is related to periodic
boundaries, I used two approaches:
1. The pull group of interest (permeant) was centered in the x-y plane
of the box using Chris' approach. I then used the genconf utility to
replicate my lipid box to a 9x9 grid in the x-y plane and removed all
but the center box. This generated the coordinates for a bilayer system
with all lipid molecules inside a box and intact. The discrepancy
between the grompp (version 4.0.3) output and distances as
calculated by
g_traj (version 4.0.3) persist, 2.667 vs. 0.3996 nm.
2. I constructed a three atom system containing 2 reference atoms of
type A, and a pull atom of type B. Proper output from grompp was
observed for all coordinates of both the reference and pulled atoms,
include coordinates for atoms moved outside the box in the x-y plane.
The coordinate, topology, and run control parameter file are given
below.
If there are additional suggestions, I would be greatly appreciative.
Thank you,
Steve Fiedler
-
conf.gro
Three atoms
3
1AAA A 1 1.500 1.500 1.000
2AAA A 2 0.500 1.500 1.000
3BBB B 3 -1.500 1.500 1.700
3.0 3.0 3.0
-
index.ndx
[ System ]
1 2 3
[ Ref ]
1 2
[ Pulled ]
3
-
grompp.mdp
title = ThreeAtoms
integrator = md
dt = 0.001
nsteps = 1
ns_type = grid
pbc = xyz
coulombtype = shift
rlist = 1.4
rcoulomb = 1.4
rvdw = 1.4
tcoupl = no
pcoupl = no
constraint_algorithm = shake
shake_tol = 1e-4
gen-vel = no
gen-temp = 0
nstxout = 1
nstvout = 0
nstfout = 0
pull = umbrella
pull_geometry = distance
pull_dim = N N Y
pull_start = no
pull_init1 = 0.7
pull_group0 = Ref
pull_group1 = Pulled
pull_k1 = 1
-
topology.top
; topology for two partially charged atoms
[ defaults ]
; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
1 3 yes 0.125 0.5
[ atomtypes ]
;name mass charge ptype sig eps
A 1000. 0.000 A 0.5 9.9
B 9. 0.000 A 0.3 9.0
[ nonbond_params ]
; i j func sig eps
[ moleculetype ]
1
[ atoms ]
; nr type resnr residue atom cgnr charge mass
1 A 1 AAA A 1 0.000 1000.
[ moleculetype ]
1
[ atoms ]
; nr type resnr residue atom cgnr charge mass
1 B 1 BBB B 1 0.000 9.00
[ system ]
; name
Three atoms
[ molecules ]
; name number
2
1
Chris Neale wrote:
I just checked similar simulations of mine and Berk's suggestion
accounts for similar discrepancies that I notice on a quick
evaluation
where g_traj and g_dist fail to give me the same distance as I obtain
from the pull pos.xvg file. As Berk suggests, once I first trjconv
-center -pbc mol -ur
[gmx-users] Transition difficulties: version 3.3.3 to 4.0.3 regarding pull_geometry=distance
Hi Steve,
Noting Berk's comment, I should clarify that my runs were completed using 4.0.2 and were run in parallel, so you may be seeing
something different than the discrepancy that I noted from g_dist or g_traj.
Did you try the post-mdrun processing and g_dist test that I suggested here:
http://www.gromacs.org/pipermail/gmx-users/2009-January/039153.html
?
Chris.
-- original message --
Hi,
I just found out that I introduced a bug in 4.0.3, which could cause
the pull code to crash or give wrong results when running single processor.
In parallel it is correct.
I committed fixed for 4.0.4.
If you run in parallel things should be correct,
or change in src/kernel/md.c:
if (ir-pull) {
dd_make_local_pull_groups(NULL,ir-pull,mdatoms);
to
if (ir-pull PAR(cr)) {
dd_make_local_pull_groups(NULL,ir-pull,mdatoms);
Berk
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Re: [gmx-users] Transition difficulties: version 3.3.3 to 4.0.3 regarding pull_geometry=distance
Hi Chris, Your suggestions were helpful. Due to the nature of this problem, there were limitations in the application of the sequence of steps that you recommended. Specifically, the difference in the equilibrated structure from version 3.3.x to the calculated reference center of mass from version 4.0.x causes an unreasonable jump with constraint force calculation. Resultant bad contacts prohibit generation of a pull output file. More generally though, I believe I understand your broader point: the sensitive nature of the periodic box with respect to the pull code and possible discrepancies in the pbc treatment by various utilities, may cause confusion with the diagnostic process. The test bilayer system I created however, centered distantly from the x and y box edges, may effectively remove this set of concerns. For example, this configuration is relatively unchanged upon recentering, however it is still susceptible to the problem that is the subject of this discussion. If I can reproduce this phenomenon with a publicly available topology file, I can provide the necessary input files for inspection. Thank you again, Steve Fiedler chris.ne...@utoronto.ca wrote: Hi Steve, what I intended to suggest was actually something different (and much easier). The idea is not that you need some special system to be able to utilize the pull code, but that the pull code is correct whereas the g_dist and g_traj programs are not as good at treating pbc in the way that one desires. I suggest the following. 1. Take your original system and run the pull code for a very short simulation. Use the last line of the output to calculate the relevant displacement 2. Now use trjconv -b -e to get the last frame of the .xtc that resulted from that short MD run as a .gro file, call it final.gro. I suspect that your groups are not entirely in the same simulation box in final.gro. 3. Now make a new .ndx file from that .gro and give it a single residue that is near your binding pocket, call it R_1 4. Now apply trjconv -center -pbc mol -ur compact while selecting R_1 for centering, call the new .gro file final_center.gro 5. Visualize final_center.gro and ensure that all of your relevant atoms are in the same image in the way that puts the minimum distance between them along a path that is entirely contained within the unit cell. If not, go back to step 3 and try making a group R_2, etc. until this process works. NOTE: you might think that giving trjconv -center the relevant groups that you use for pulling will be a good idea here, but it is not. The problem there is that the atoms may be centered by placing half on the left boundary and half on the right boundary. I find using one logically selected residue or atom is the best method here. 6. Assuming that you got what you wanted in step 5, now run g_traj and g_dist on final_center.gro. In my case, I found that g_traj and g_dist give the same answer as the pull code output when I am using final_center.gro, but not always when I am using final.gro. *** I always laugh when these problems arise because, in an important sense, the protein *did* jump out of the simulation box... at least as far as g_traj and g_dist are concerned. This, we must hope, is correctly treated in the pull code even though it is incorrectly (or at least unintuitively) treated by g_traj and g_dist. Chris. -- original message -- Hi, Thank you Berk and Chris for the suggestions. To address the possibility that this issue is related to periodic boundaries, I used two approaches: 1. The pull group of interest (permeant) was centered in the x-y plane of the box using Chris' approach. I then used the genconf utility to replicate my lipid box to a 9x9 grid in the x-y plane and removed all but the center box. This generated the coordinates for a bilayer system with all lipid molecules inside a box and intact. The discrepancy between the grompp (version 4.0.3) output and distances as calculated by g_traj (version 4.0.3) persist, 2.667 vs. 0.3996 nm. 2. I constructed a three atom system containing 2 reference atoms of type A, and a pull atom of type B. Proper output from grompp was observed for all coordinates of both the reference and pulled atoms, include coordinates for atoms moved outside the box in the x-y plane. The coordinate, topology, and run control parameter file are given below. If there are additional suggestions, I would be greatly appreciative. Thank you, Steve Fiedler - conf.gro Three atoms 3 1AAA A1 1.500 1.500 1.000 2AAA A2 0.500 1.500 1.000 3BBB B3 -1.500 1.500 1.700 3.0 3.0 3.0 - index.ndx [ System ] 123 [ Ref ] 12 [ Pulled ] 3 - grompp.mdp title= ThreeAtoms integrator = md dt = 0.001 nsteps = 1
Re: [gmx-users] Transition difficulties: version 3.3.3 to 4.0.3 regarding pull_geometry=distance
Hi,
I rebuilt the code using both sets of Berk's corrections. On an
isolated bilayer system with no periodic boundaries in the x-y plane
prepared in the manner previously explained, the recompiled grompp
output yielded no improvement in the discrepancies of the position of a
buckyball permeant. By visual inspection, it appears that the 4.0.x
versions still attempt to distort the position of the permeant
significant upward from the bilayer center, i.e., the center of mass of
the reference group. Interestingly, the 3.3.x and 4.0.x version
identically treated a test bilayer system constructed with a single
dummy particle permeant.
I appreciate the help of Berk, and Chris' detailed suggestions with this
interesting problem.
Sincerely,
Steve Fiedler
Berk Hess wrote:
Hi,
I just found out that I introduced a bug in 4.0.3, which could cause
the pull code to crash or give wrong results when running single
processor.
In parallel it is correct.
I committed fixed for 4.0.4.
If you run in parallel things should be correct,
or change in src/kernel/md.c:
if (ir-pull) {
dd_make_local_pull_groups(NULL,ir-pull,mdatoms);
to
if (ir-pull PAR(cr)) {
dd_make_local_pull_groups(NULL,ir-pull,mdatoms);
Berk
Date: Fri, 23 Jan 2009 12:14:43 -0500
From: fied...@umich.edu
To: gmx-users@gromacs.org
Subject: Re: [gmx-users] Transition difficulties: version 3.3.3 to
4.0.3 regarding pull_geometry=distance
Hi,
Thank you Berk and Chris for the suggestions.
To address the possibility that this issue is related to periodic
boundaries, I used two approaches:
1. The pull group of interest (permeant) was centered in the x-y plane
of the box using Chris' approach. I then used the genconf utility to
replicate my lipid box to a 9x9 grid in the x-y plane and removed all
but the center box. This generated the coordinates for a bilayer system
with all lipid molecules inside a box and intact. The discrepancy
between the grompp (version 4.0.3) output and distances as
calculated by
g_traj (version 4.0.3) persist, 2.667 vs. 0.3996 nm.
2. I constructed a three atom system containing 2 reference atoms of
type A, and a pull atom of type B. Proper output from grompp was
observed for all coordinates of both the reference and pulled atoms,
include coordinates for atoms moved outside the box in the x-y plane.
The coordinate, topology, and run control parameter file are given
below.
If there are additional suggestions, I would be greatly appreciative.
Thank you,
Steve Fiedler
-
conf.gro
Three atoms
3
1AAA A 1 1.500 1.500 1.000
2AAA A 2 0.500 1.500 1.000
3BBB B 3 -1.500 1.500 1.700
3.0 3.0 3.0
-
index.ndx
[ System ]
1 2 3
[ Ref ]
1 2
[ Pulled ]
3
-
grompp.mdp
title = ThreeAtoms
integrator = md
dt = 0.001
nsteps = 1
ns_type = grid
pbc = xyz
coulombtype = shift
rlist = 1.4
rcoulomb = 1.4
rvdw = 1.4
tcoupl = no
pcoupl = no
constraint_algorithm = shake
shake_tol = 1e-4
gen-vel = no
gen-temp = 0
nstxout = 1
nstvout = 0
nstfout = 0
pull = umbrella
pull_geometry = distance
pull_dim = N N Y
pull_start = no
pull_init1 = 0.7
pull_group0 = Ref
pull_group1 = Pulled
pull_k1 = 1
-
topology.top
; topology for two partially charged atoms
[ defaults ]
; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
1 3 yes 0.125 0.5
[ atomtypes ]
;name mass charge ptype sig eps
A 1000. 0.000 A 0.5 9.9
B 9. 0.000 A 0.3 9.0
[ nonbond_params ]
; i j func sig eps
[ moleculetype ]
1
[ atoms ]
; nr type resnr residue atom cgnr charge mass
1 A 1 AAA A 1 0.000 1000.
[ moleculetype ]
1
[ atoms ]
; nr type resnr residue atom cgnr charge mass
1 B 1 BBB B 1 0.000 9.00
[ system ]
; name
Three atoms
[ molecules ]
; name number
2
1
Chris Neale wrote:
I just checked similar simulations of mine and Berk's suggestion
accounts for similar discrepancies that I notice on a quick
evaluation
where g_traj and g_dist fail to give me the same distance as I obtain
from the pull pos.xvg file. As Berk suggests, once I first trjconv
-center -pbc mol -ur compact (giving an appropriate residue for
centering that puts all relevant pulled atoms in the same box) then
g_traj and g_dist both give me the exact same answer as I calculate
based on pull pos.xvg. Chris -- original message -- Hi, There
could be
a problem with periodic boundary conditions. Do you have multiple
molecules in a pull group, or broken molecules? In that case the COM
position of 3.3.3 and g_traj are both incorrect. The pull code in 4.0
grompp and mdrun are (as far as I know) always correct. Berk
Date: Thu, 22 Jan 2009 13:22:24 -0500
From: fied...@umich.edu
To: gmx-users@gromacs.org
Subject: [gmx-users] Transition difficulties: version 3.3.3 to
4.0.3 regarding pull_geometry=distance
Dear all,
I have encountered
RE: [gmx-users] Transition difficulties: version 3.3.3 to 4.0.3 regarding pull_geometry=distance
Hi,
I just found out that I introduced a bug in 4.0.3, which could cause
the pull code to crash or give wrong results when running single processor.
In parallel it is correct.
I committed fixed for 4.0.4.
If you run in parallel things should be correct,
or change in src/kernel/md.c:
if (ir-pull) {
dd_make_local_pull_groups(NULL,ir-pull,mdatoms);
to
if (ir-pull PAR(cr)) {
dd_make_local_pull_groups(NULL,ir-pull,mdatoms);
Berk
Date: Fri, 23 Jan 2009 12:14:43 -0500
From: fied...@umich.edu
To: gmx-users@gromacs.org
Subject: Re: [gmx-users] Transition difficulties: version 3.3.3 to4.0.3
regarding pull_geometry=distance
Hi,
Thank you Berk and Chris for the suggestions.
To address the possibility that this issue is related to periodic
boundaries, I used two approaches:
1. The pull group of interest (permeant) was centered in the x-y plane
of the box using Chris' approach. I then used the genconf utility to
replicate my lipid box to a 9x9 grid in the x-y plane and removed all
but the center box. This generated the coordinates for a bilayer system
with all lipid molecules inside a box and intact. The discrepancy
between the grompp (version 4.0.3) output and distances as calculated by
g_traj (version 4.0.3) persist, 2.667 vs. 0.3996 nm.
2. I constructed a three atom system containing 2 reference atoms of
type A, and a pull atom of type B. Proper output from grompp was
observed for all coordinates of both the reference and pulled atoms,
include coordinates for atoms moved outside the box in the x-y plane.
The coordinate, topology, and run control parameter file are given below.
If there are additional suggestions, I would be greatly appreciative.
Thank you,
Steve Fiedler
-
conf.gro
Three atoms
3
1AAA A1 1.500 1.500 1.000
2AAA A2 0.500 1.500 1.000
3BBB B3 -1.500 1.500 1.700
3.0 3.0 3.0
-
index.ndx
[ System ]
123
[ Ref ]
12
[ Pulled ]
3
-
grompp.mdp
title= ThreeAtoms
integrator = md
dt = 0.001
nsteps = 1
ns_type = grid
pbc = xyz
coulombtype = shift
rlist= 1.4
rcoulomb = 1.4
rvdw = 1.4
tcoupl = no
pcoupl = no
constraint_algorithm = shake
shake_tol= 1e-4
gen-vel = no
gen-temp = 0
nstxout = 1
nstvout = 0
nstfout = 0
pull = umbrella
pull_geometry = distance
pull_dim = N N Y
pull_start = no
pull_init1 = 0.7
pull_group0 = Ref
pull_group1 = Pulled
pull_k1 = 1
-
topology.top
; topology for two partially charged atoms
[ defaults ]
; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
1 3 yes 0.125 0.5
[ atomtypes ]
;name mass charge ptype sig eps
A 1000.0.000 A 0.5 9.9
B 9.0.000 A 0.3 9.0
[ nonbond_params ]
; ijfuncsig eps
[ moleculetype ]
1
[ atoms ]
; nr type resnr residue atom cgnr charge mass
1 A 1 AAAA 1 0.000 1000.
[ moleculetype ]
1
[ atoms ]
; nr type resnr residue atom cgnr charge mass
1 B 1 BBBB 1 0.000 9.00
[ system ]
; name
Three atoms
[ molecules ]
; name number
2
1
Chris Neale wrote:
I just checked similar simulations of mine and Berk's suggestion
accounts for similar discrepancies that I notice on a quick evaluation
where g_traj and g_dist fail to give me the same distance as I obtain
from the pull pos.xvg file. As Berk suggests, once I first trjconv
-center -pbc mol -ur compact (giving an appropriate residue for
centering that puts all relevant pulled atoms in the same box) then
g_traj and g_dist both give me the exact same answer as I calculate
based on pull pos.xvg. Chris -- original message -- Hi, There could be
a problem with periodic boundary conditions. Do you have multiple
molecules in a pull group, or broken molecules? In that case the COM
position of 3.3.3 and g_traj are both incorrect. The pull code in 4.0
grompp and mdrun are (as far as I know) always correct. Berk
Date: Thu, 22 Jan 2009 13:22:24 -0500
From: fied...@umich.edu
To: gmx-users@gromacs.org
Subject: [gmx-users] Transition difficulties: version 3.3.3 to
4.0.3regarding pull_geometry=distance
Dear all,
I have encountered an odd behavior with use of the pull_geometry
= distance option of the pull code, upon transitioning from
Gromacs version 3.3.3 to version
Re: [gmx-users] Transition difficulties: version 3.3.3 to 4.0.3 regarding pull_geometry=distance
Hi, Thank you Berk and Chris for the suggestions. To address the possibility that this issue is related to periodic boundaries, I used two approaches: 1. The pull group of interest (permeant) was centered in the x-y plane of the box using Chris' approach. I then used the genconf utility to replicate my lipid box to a 9x9 grid in the x-y plane and removed all but the center box. This generated the coordinates for a bilayer system with all lipid molecules inside a box and intact. The discrepancy between the grompp (version 4.0.3) output and distances as calculated by g_traj (version 4.0.3) persist, 2.667 vs. 0.3996 nm. 2. I constructed a three atom system containing 2 reference atoms of type A, and a pull atom of type B. Proper output from grompp was observed for all coordinates of both the reference and pulled atoms, include coordinates for atoms moved outside the box in the x-y plane. The coordinate, topology, and run control parameter file are given below. If there are additional suggestions, I would be greatly appreciative. Thank you, Steve Fiedler - conf.gro Three atoms 3 1AAA A1 1.500 1.500 1.000 2AAA A2 0.500 1.500 1.000 3BBB B3 -1.500 1.500 1.700 3.0 3.0 3.0 - index.ndx [ System ] 123 [ Ref ] 12 [ Pulled ] 3 - grompp.mdp title= ThreeAtoms integrator = md dt = 0.001 nsteps = 1 ns_type = grid pbc = xyz coulombtype = shift rlist= 1.4 rcoulomb = 1.4 rvdw = 1.4 tcoupl = no pcoupl = no constraint_algorithm = shake shake_tol= 1e-4 gen-vel = no gen-temp = 0 nstxout = 1 nstvout = 0 nstfout = 0 pull = umbrella pull_geometry = distance pull_dim = N N Y pull_start = no pull_init1 = 0.7 pull_group0 = Ref pull_group1 = Pulled pull_k1 = 1 - topology.top ; topology for two partially charged atoms [ defaults ] ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ 1 3 yes 0.125 0.5 [ atomtypes ] ;name mass charge ptype sig eps A 1000.0.000 A 0.5 9.9 B 9.0.000 A 0.3 9.0 [ nonbond_params ] ; ijfuncsig eps [ moleculetype ] 1 [ atoms ] ; nr type resnr residue atom cgnr charge mass 1 A 1 AAAA 1 0.000 1000. [ moleculetype ] 1 [ atoms ] ; nr type resnr residue atom cgnr charge mass 1 B 1 BBBB 1 0.000 9.00 [ system ] ; name Three atoms [ molecules ] ; name number 2 1 Chris Neale wrote: I just checked similar simulations of mine and Berk's suggestion accounts for similar discrepancies that I notice on a quick evaluation where g_traj and g_dist fail to give me the same distance as I obtain from the pull pos.xvg file. As Berk suggests, once I first trjconv -center -pbc mol -ur compact (giving an appropriate residue for centering that puts all relevant pulled atoms in the same box) then g_traj and g_dist both give me the exact same answer as I calculate based on pull pos.xvg. Chris -- original message -- Hi, There could be a problem with periodic boundary conditions. Do you have multiple molecules in a pull group, or broken molecules? In that case the COM position of 3.3.3 and g_traj are both incorrect. The pull code in 4.0 grompp and mdrun are (as far as I know) always correct. Berk Date: Thu, 22 Jan 2009 13:22:24 -0500 From: fied...@umich.edu To: gmx-users@gromacs.org Subject: [gmx-users] Transition difficulties: version 3.3.3 to 4.0.3regarding pull_geometry=distance Dear all, I have encountered an odd behavior with use of the pull_geometry = distance option of the pull code, upon transitioning from Gromacs version 3.3.3 to version 4.0.3. It appears to be related to the center of mass distances of the two pull groups, which has an effect of abruptly displacing the coordinates of the less massive group. A diagnostic is a discrepancy between the distances between the pull groups from the preprocessor output in version 4.0.3, and the distance between the groups as calculated using the difference of the groups' centers of mass from the g_traj utility. For example, using the coordinates of a system previously equilibrated with the constraint force approach from version 3.3.3, the grompp output from version 4.0.3 is: Pull group natoms pbc atom distance at start reference at t=0 0 2672 1336 160 6818 2.673 0.400 Using g_traj (4.0.3 version), the difference
[gmx-users] Transition difficulties: version 3.3.3 to 4.0.3 regarding pull_geometry=distance
Hi Steve, what I intended to suggest was actually something different (and much easier). The idea is not that you need some special system to be able to utilize the pull code, but that the pull code is correct whereas the g_dist and g_traj programs are not as good at treating pbc in the way that one desires. I suggest the following. 1. Take your original system and run the pull code for a very short simulation. Use the last line of the output to calculate the relevant displacement 2. Now use trjconv -b -e to get the last frame of the .xtc that resulted from that short MD run as a .gro file, call it final.gro. I suspect that your groups are not entirely in the same simulation box in final.gro. 3. Now make a new .ndx file from that .gro and give it a single residue that is near your binding pocket, call it R_1 4. Now apply trjconv -center -pbc mol -ur compact while selecting R_1 for centering, call the new .gro file final_center.gro 5. Visualize final_center.gro and ensure that all of your relevant atoms are in the same image in the way that puts the minimum distance between them along a path that is entirely contained within the unit cell. If not, go back to step 3 and try making a group R_2, etc. until this process works. NOTE: you might think that giving trjconv -center the relevant groups that you use for pulling will be a good idea here, but it is not. The problem there is that the atoms may be centered by placing half on the left boundary and half on the right boundary. I find using one logically selected residue or atom is the best method here. 6. Assuming that you got what you wanted in step 5, now run g_traj and g_dist on final_center.gro. In my case, I found that g_traj and g_dist give the same answer as the pull code output when I am using final_center.gro, but not always when I am using final.gro. *** I always laugh when these problems arise because, in an important sense, the protein *did* jump out of the simulation box... at least as far as g_traj and g_dist are concerned. This, we must hope, is correctly treated in the pull code even though it is incorrectly (or at least unintuitively) treated by g_traj and g_dist. Chris. -- original message -- Hi, Thank you Berk and Chris for the suggestions. To address the possibility that this issue is related to periodic boundaries, I used two approaches: 1. The pull group of interest (permeant) was centered in the x-y plane of the box using Chris' approach. I then used the genconf utility to replicate my lipid box to a 9x9 grid in the x-y plane and removed all but the center box. This generated the coordinates for a bilayer system with all lipid molecules inside a box and intact. The discrepancy between the grompp (version 4.0.3) output and distances as calculated by g_traj (version 4.0.3) persist, 2.667 vs. 0.3996 nm. 2. I constructed a three atom system containing 2 reference atoms of type A, and a pull atom of type B. Proper output from grompp was observed for all coordinates of both the reference and pulled atoms, include coordinates for atoms moved outside the box in the x-y plane. The coordinate, topology, and run control parameter file are given below. If there are additional suggestions, I would be greatly appreciative. Thank you, Steve Fiedler - conf.gro Three atoms 3 1AAA A1 1.500 1.500 1.000 2AAA A2 0.500 1.500 1.000 3BBB B3 -1.500 1.500 1.700 3.0 3.0 3.0 - index.ndx [ System ] 123 [ Ref ] 12 [ Pulled ] 3 - grompp.mdp title= ThreeAtoms integrator = md dt = 0.001 nsteps = 1 ns_type = grid pbc = xyz coulombtype = shift rlist= 1.4 rcoulomb = 1.4 rvdw = 1.4 tcoupl = no pcoupl = no constraint_algorithm = shake shake_tol= 1e-4 gen-vel = no gen-temp = 0 nstxout = 1 nstvout = 0 nstfout = 0 pull = umbrella pull_geometry = distance pull_dim = N N Y pull_start = no pull_init1 = 0.7 pull_group0 = Ref pull_group1 = Pulled pull_k1 = 1 - topology.top ; topology for two partially charged atoms [ defaults ] ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ 1 3 yes 0.125 0.5 [ atomtypes ] ;name mass charge ptype sig eps A 1000.0.000 A 0.5 9.9 B 9.0.000 A 0.3 9.0 [ nonbond_params ] ; ijfuncsig eps [ moleculetype ] 1 [ atoms ] ; nr type resnr residue atom cgnr charge mass 1 A 1 AAAA 1 0.000 1000. [ moleculetype ]
[gmx-users] Transition difficulties: version 3.3.3 to 4.0.3 regarding pull_geometry=distance
Dear all, I have encountered an odd behavior with use of the pull_geometry = distance option of the pull code, upon transitioning from Gromacs version 3.3.3 to version 4.0.3. It appears to be related to the center of mass distances of the two pull groups, which has an effect of abruptly displacing the coordinates of the less massive group. A diagnostic is a discrepancy between the distances between the pull groups from the preprocessor output in version 4.0.3, and the distance between the groups as calculated using the difference of the groups' centers of mass from the g_traj utility. For example, using the coordinates of a system previously equilibrated with the constraint force approach from version 3.3.3, the grompp output from version 4.0.3 is: Pull group natoms pbc atom distance at start reference at t=0 0 2672 1336 160 6818 2.673 0.400 Using g_traj (4.0.3 version), the difference of the distance between the center of masses of the two groups is: 0.39911 nm versus the 2.673 value from above. This issue does not exist in previous versions of Gromacs including version 3.3.3. In version 4.0.3, this behavior occurs for both pull=umbrella and pull = constraint, on 32 and 64 bit architecture systems, and in both single and double precision calculations. A test of a two atom system determined that the pull_start option was not appropriate. The pull options used in the mdp file are listed below, as well as the contents of the ppa file which has worked previously. Suggestions would be appreciated, Thank you, Steve Fiedler Gromacs 4.0.0 mdp pull options pull = constraint pull_geometry = distance pull_dim = N N Y pull_start = no pull_init1 = .4 pull_group0 = Ref pull_group1 = Buk Gromacs 3.3.3 ppa file: runtype = constraint group_1 = BUK reference_group = Ref reftype = com constraint_direction = 0 0 1 constraint_distance1 = 0.400 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] Transition difficulties: version 3.3.3 to 4.0.3 regarding pull_geometry=distance
Hi, There could be a problem with periodic boundary conditions. Do you have multiple molecules in a pull group, or broken molecules? In that case the COM position of 3.3.3 and g_traj are both incorrect. The pull code in 4.0 grompp and mdrun are (as far as I know) always correct. Berk Date: Thu, 22 Jan 2009 13:22:24 -0500 From: fied...@umich.edu To: gmx-users@gromacs.org Subject: [gmx-users] Transition difficulties: version 3.3.3 to 4.0.3 regarding pull_geometry=distance Dear all, I have encountered an odd behavior with use of the pull_geometry = distance option of the pull code, upon transitioning from Gromacs version 3.3.3 to version 4.0.3. It appears to be related to the center of mass distances of the two pull groups, which has an effect of abruptly displacing the coordinates of the less massive group. A diagnostic is a discrepancy between the distances between the pull groups from the preprocessor output in version 4.0.3, and the distance between the groups as calculated using the difference of the groups' centers of mass from the g_traj utility. For example, using the coordinates of a system previously equilibrated with the constraint force approach from version 3.3.3, the grompp output from version 4.0.3 is: Pull group natoms pbc atom distance at start reference at t=0 0 2672 1336 160 6818 2.673 0.400 Using g_traj (4.0.3 version), the difference of the distance between the center of masses of the two groups is: 0.39911 nm versus the 2.673 value from above. This issue does not exist in previous versions of Gromacs including version 3.3.3. In version 4.0.3, this behavior occurs for both pull=umbrella and pull = constraint, on 32 and 64 bit architecture systems, and in both single and double precision calculations. A test of a two atom system determined that the pull_start option was not appropriate. The pull options used in the mdp file are listed below, as well as the contents of the ppa file which has worked previously. Suggestions would be appreciated, Thank you, Steve Fiedler Gromacs 4.0.0 mdp pull options pull = constraint pull_geometry = distance pull_dim = N N Y pull_start = no pull_init1 = .4 pull_group0 = Ref pull_group1 = Buk Gromacs 3.3.3 ppa file: runtype = constraint group_1 = BUK reference_group = Ref reftype = com constraint_direction = 0 0 1 constraint_distance1 = 0.400 ___ 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 _ Express yourself instantly with MSN Messenger! Download today it's FREE! http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/___ 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] Transition difficulties: version 3.3.3 to 4.0.3 regarding pull_geometry=distance
I just checked similar simulations of mine and Berk's suggestion accounts for similar discrepancies that I notice on a quick evaluation where g_traj and g_dist fail to give me the same distance as I obtain from the pull pos.xvg file. As Berk suggests, once I first trjconv -center -pbc mol -ur compact (giving an appropriate residue for centering that puts all relevant pulled atoms in the same box) then g_traj and g_dist both give me the exact same answer as I calculate based on pull pos.xvg. Chris -- original message -- Hi, There could be a problem with periodic boundary conditions. Do you have multiple molecules in a pull group, or broken molecules? In that case the COM position of 3.3.3 and g_traj are both incorrect. The pull code in 4.0 grompp and mdrun are (as far as I know) always correct. Berk Date: Thu, 22 Jan 2009 13:22:24 -0500 From: fied...@umich.edu To: gmx-users@gromacs.org Subject: [gmx-users] Transition difficulties: version 3.3.3 to 4.0.3 regarding pull_geometry=distance Dear all, I have encountered an odd behavior with use of the pull_geometry = distance option of the pull code, upon transitioning from Gromacs version 3.3.3 to version 4.0.3. It appears to be related to the center of mass distances of the two pull groups, which has an effect of abruptly displacing the coordinates of the less massive group. A diagnostic is a discrepancy between the distances between the pull groups from the preprocessor output in version 4.0.3, and the distance between the groups as calculated using the difference of the groups' centers of mass from the g_traj utility. For example, using the coordinates of a system previously equilibrated with the constraint force approach from version 3.3.3, the grompp output from version 4.0.3 is: Pull group natoms pbc atom distance at start reference at t=0 0 2672 1336 160 6818 2.673 0.400 Using g_traj (4.0.3 version), the difference of the distance between the center of masses of the two groups is: 0.39911 nm versus the 2.673 value from above. This issue does not exist in previous versions of Gromacs including version 3.3.3. In version 4.0.3, this behavior occurs for both pull=umbrella and pull = constraint, on 32 and 64 bit architecture systems, and in both single and double precision calculations. A test of a two atom system determined that the pull_start option was not appropriate. The pull options used in the mdp file are listed below, as well as the contents of the ppa file which has worked previously. Suggestions would be appreciated, ___ 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
