RE: [gmx-users] Umbrella sampling PMF, drug and membrane with pull_geometry=cylinder
Hello, I assume that you mean pull_pbcatom0... Nothing changes when I set this to an atom index I am afraid. I saw that you had use pull_geometry=cylinder in your recent JACS paper. Would it be too much to ask to see those pull settings? I simply cannot get the molecule to stay at the desired z-position... Thanks! > Hi, > > we had similar trouble some time ago, and we could solve it by using a > good PBC atom. Make sure that your pbc_atom is in the very center of > your membrane. > > Btw, using "distance" to compare with "cylinder" is a bad test, since it > does something very different (the distance is the same at z=com-1 and > z=com+1. I would use "direction" or "position" for your test. You can > also use position/direction for the umbrella simulations, you'll > probably get similar results to the geometry "cylinder", but you'll also > have to make sure your pbc_atom is fine. > > Cheers, > Jochen -- 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 PMF, drug and membrane with pull_geometry=cylinder
Hi, we had similar trouble some time ago, and we could solve it by using a good PBC atom. Make sure that your pbc_atom is in the very center of your membrane. Btw, using "distance" to compare with "cylinder" is a bad test, since it does something very different (the distance is the same at z=com-1 and z=com+1. I would use "direction" or "position" for your test. You can also use position/direction for the umbrella simulations, you'll probably get similar results to the geometry "cylinder", but you'll also have to make sure your pbc_atom is fine. Cheers, Jochen Am 4/29/12 9:20 PM, schrieb J B: > Does the cylinder geometry work if you use "pull_start = no" and pull_init1 > equal to your starting (restraint) distance? I'm just trying to go through all > of the iterations of what might be failing. In theory, what you're doing is > fine but I'd be interested to know if there was something failing in the input > parsing such that pull_start is not being properly applied. The screen output > of grompp will also tell you what it believes the restraint distance is. If it > prints 0, then there's a problem with input processing. > > If the problem is reproducible in the latest Gromacs version (4.5.5), please > file a bug report on redmine.gromacs.org so that it can be investigated. Please > provide .tpr file of the system so that the developers can run what you are > trying to do and see. > > -Justin It works if I set pull_start to the initial distance given by g_dist things work just fine. So this will be the way for now at least. Guess that there could be an error in the inout parsing then. Thanks a lot for your help, really appreciate it. -- --- Dr. Jochen Hub Computational Molecular Biophysics Group Institute for Microbiology and Genetics Georg-August-University of Göttingen Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany. Phone: +49-551-39-14189 http://cmb.bio.uni-goettingen.de/ --- -- 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 PMF, drug and membrane with pull_geometry=cylinder
> Does the cylinder geometry work if you use "pull_start = no" and pull_init1 > equal to your starting (restraint) distance? I'm just trying to go through > all > of the iterations of what might be failing. In theory, what you're doing is > fine but I'd be interested to know if there was something failing in the > input > parsing such that pull_start is not being properly applied. The screen > output > of grompp will also tell you what it believes the restraint distance is. If > it > prints 0, then there's a problem with input processing. > > If the problem is reproducible in the latest Gromacs version (4.5.5), please > file a bug report on redmine.gromacs.org so that it can be investigated. > Please > provide .tpr file of the system so that the developers can run what you are > trying to do and see. > > -Justin It works if I set pull_start to the initial distance given by g_dist things work just fine. So this will be the way for now at least. Guess that there could be an error in the inout parsing then. Thanks a lot for your help, really appreciate it. -- 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 PMF, drug and membrane with pull_geometry=cylinder
On 4/29/12 4:46 AM, J B wrote: > Is the problem specific to cylinder geometry? Do other settings work? Does it > make a difference if you set values for pull_r0 and pull_r1? > > -Justin I would think that it is the cylinder geometry that creates the problem. If I use pull = umbrella pull_geometry = distance pull_dim = N N Y pull_start = yes pull_init1= 0.0 pull_ngroups = 1 pull_group0 = DPPC pull_group1 = drug pull_rate1 = 0.0 The molecules stays in place. But pull_geometry=distance is what I would prefer due to the undulations. Changing pull_r0 and pull_r1 still makes the drug molecule move down towards the membrane... Does the cylinder geometry work if you use "pull_start = no" and pull_init1 equal to your starting (restraint) distance? I'm just trying to go through all of the iterations of what might be failing. In theory, what you're doing is fine but I'd be interested to know if there was something failing in the input parsing such that pull_start is not being properly applied. The screen output of grompp will also tell you what it believes the restraint distance is. If it prints 0, then there's a problem with input processing. If the problem is reproducible in the latest Gromacs version (4.5.5), please file a bug report on redmine.gromacs.org so that it can be investigated. Please provide .tpr file of the system so that the developers can run what you are trying to do and see. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] Umbrella sampling PMF, drug and membrane with pull_geometry=cylinder
> Is the problem specific to cylinder geometry? Do other settings work? Does > it > make a difference if you set values for pull_r0 and pull_r1? > > -Justin I would think that it is the cylinder geometry that creates the problem. If I use pull= umbrellapull_geometry = distancepull_dim = N N Ypull_start = yespull_init1 = 0.0pull_ngroups = 1pull_group0 = DPPCpull_group1 = drugpull_rate1= 0.0 The molecules stays in place. But pull_geometry=distance is what I would prefer due to the undulations. Changing pull_r0 and pull_r1 still makes the drug molecule move down towards the membrane... -- 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 PMF, drug and membrane with pull_geometry=cylinder
On 4/28/12 12:28 PM, J B wrote: Hi, the distance is 3.89 nm and the z-dimension is roughly 8 nm Is the problem specific to cylinder geometry? Do other settings work? Does it make a difference if you set values for pull_r0 and pull_r1? -Justin > Date: Sat, 28 Apr 2012 09:18:31 -0400 > From: jalem...@vt.edu > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] Umbrella sampling PMF, drug and membrane with pull_geometry=cylinder > > > > On 4/28/12 5:12 AM, J B wrote: > > Hi. > > > > I am trying to the the PMF of transferring a drug molecule from the aqueous > > phase to a lipid bilayer. > > > > In order to minimize the effects of membrane undulations I tried to use > > pull_geometry=cylinder. > > > > Whenever I run a short simulation with umbrella sampling starting from a > > configuration with the drug molecule way above the bilayer > > the drug molecule is pulled into the bilayer rather rapidly. It appears as if > > the distance between the cylinder's COM and > > the drug molecule's COM is supposed to be zero since it is pulled to the center > > of the membrane. > > > > Since I apply an umbrella potential I find this weird and I would of course like > > the molecule to > > "stay put" at that current z-position. Probably I set up the pull code wrong. > > Here are my options: > > > > pull = umbrella > > pull_geometry = cylinder > > pull_dim = N N Y > > pull_ngroups = 1 > > pull_rate1 = 0.0 > > pull_k1 = 1000 > > pull_start = yes > > pull_init1 = 0.0 > > pull_vec1 = 0.0 0.0 1.0 > > pull_pbcatom0 = 0 > > pull_ngroups = 1 > > pull_group0 = DPPC > > pull_group1 = drug > > > > Have not decided the radii of the cylinder yet, but that is besides the point here. > > > > I run with the 4.5.5 version and cannot figure what the problem is. > > > > What is the initial distance between the drug and membrane, as measured by > g_dist? What is the length of your unit cell along the z-axis? > > -Justin > > -- > > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > 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 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] Umbrella sampling PMF, drug and membrane with pull_geometry=cylinder
Hi, the distance is 3.89 nm and the z-dimension is roughly 8 nm > Date: Sat, 28 Apr 2012 09:18:31 -0400 > From: jalem...@vt.edu > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] Umbrella sampling PMF, drug and membrane with > pull_geometry=cylinder > > > > On 4/28/12 5:12 AM, J B wrote: > > Hi. > > > > I am trying to the the PMF of transferring a drug molecule from the aqueous > > phase to a lipid bilayer. > > > > In order to minimize the effects of membrane undulations I tried to use > > pull_geometry=cylinder. > > > > Whenever I run a short simulation with umbrella sampling starting from a > > configuration with the drug molecule way above the bilayer > > the drug molecule is pulled into the bilayer rather rapidly. It appears as > > if > > the distance between the cylinder's COM and > > the drug molecule's COM is supposed to be zero since it is pulled to the > > center > > of the membrane. > > > > Since I apply an umbrella potential I find this weird and I would of course > > like > > the molecule to > > "stay put" at that current z-position. Probably I set up the pull code > > wrong. > > Here are my options: > > > > pull = umbrella > > pull_geometry = cylinder > > pull_dim = N N Y > > pull_ngroups = 1 > > pull_rate1 = 0.0 > > pull_k1 = 1000 > > pull_start = yes > > pull_init1 = 0.0 > > pull_vec1 = 0.0 0.0 1.0 > > pull_pbcatom0 = 0 > > pull_ngroups = 1 > > pull_group0 = DPPC > > pull_group1 = drug > > > > Have not decided the radii of the cylinder yet, but that is besides the > > point here. > > > > I run with the 4.5.5 version and cannot figure what the problem is. > > > > What is the initial distance between the drug and membrane, as measured by > g_dist? What is the length of your unit cell along the z-axis? > > -Justin > > -- > > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Umbrella sampling PMF, drug and membrane with pull_geometry=cylinder
On 4/28/12 5:12 AM, J B wrote: Hi. I am trying to the the PMF of transferring a drug molecule from the aqueous phase to a lipid bilayer. In order to minimize the effects of membrane undulations I tried to use pull_geometry=cylinder. Whenever I run a short simulation with umbrella sampling starting from a configuration with the drug molecule way above the bilayer the drug molecule is pulled into the bilayer rather rapidly. It appears as if the distance between the cylinder's COM and the drug molecule's COM is supposed to be zero since it is pulled to the center of the membrane. Since I apply an umbrella potential I find this weird and I would of course like the molecule to "stay put" at that current z-position. Probably I set up the pull code wrong. Here are my options: pull = umbrella pull_geometry = cylinder pull_dim = N N Y pull_ngroups = 1 pull_rate1 = 0.0 pull_k1 = 1000 pull_start = yes pull_init1 = 0.0 pull_vec1 = 0.0 0.0 1.0 pull_pbcatom0 = 0 pull_ngroups = 1 pull_group0 = DPPC pull_group1 = drug Have not decided the radii of the cylinder yet, but that is besides the point here. I run with the 4.5.5 version and cannot figure what the problem is. What is the initial distance between the drug and membrane, as measured by g_dist? What is the length of your unit cell along the z-axis? -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Umbrella sampling PMF, drug and membrane with pull_geometry=cylinder
Hi. I am trying to the the PMF of transferring a drug molecule from the aqueous phase to a lipid bilayer. In order to minimize the effects of membrane undulations I tried to use pull_geometry=cylinder. Whenever I run a short simulation with umbrella sampling starting from a configuration with the drug molecule way above the bilayerthe drug molecule is pulled into the bilayer rather rapidly. It appears as if the distance between the cylinder's COM and the drug molecule's COM is supposed to be zero since it is pulled to the center of the membrane. Since I apply an umbrella potential I find this weird and I would of course like the molecule to"stay put" at that current z-position. Probably I set up the pull code wrong. Here are my options: pull= umbrellapull_geometry = cylinderpull_dim = N N Ypull_ngroups = 1pull_rate1 = 0.0pull_k1 = 1000pull_start= yespull_init1 = 0.0pull_vec1 = 0.0 0.0 1.0pull_pbcatom0 = 0pull_ngroups= 1pull_group0 = DPPCpull_group1 = drug Have not decided the radii of the cylinder yet, but that is besides the point here. I run with the 4.5.5 version and cannot figure what the problem is. -- 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
