[gmx-users] Umbrella Sampling tutorial
Dear Justin Thanks for your reply. You are right. I should not extrapolate too literally from your tutorial to my system. But, I have a general question: There is 2 groups in COM pulling method (reference group + pull group). If I want to use pull_geometry = distance, so, I should fix reference group to be immobile. Is it true? On the other hand, I want to know exactly using position restraining on reference group is optional or mandatory in COM pulling method? Best wishes -- 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 tutorial
On 11/10/13 5:31 AM, shahab shariati wrote: Dear Justin Thanks for your reply. You are right. I should not extrapolate too literally from your tutorial to my system. But, I have a general question: There is 2 groups in COM pulling method (reference group + pull group). If I want to use pull_geometry = distance, so, I should fix reference group to be immobile. Is it true? What you described earlier should not be attempted with distance geometry. It won't work very well. The use of restraints is almost NEVER necessary, especially in the case where the reference group is much more massive than the pulling group. On the other hand, I want to know exactly using position restraining on reference group is optional or mandatory in COM pulling method? Almost never used. More explicitly - you do not need position restraints. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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 tutorial
Dear Justin Very thanks for your reply. What you described earlier should not be attempted with distance geometry. It won't work very well. The use of restraints is almost NEVER necessary, especially in the case where the reference group is much more massive than the pulling group. I want to calculate Potential of mean force as a function of the distance between the centers of mass of drug and the lipid bilayer. You said distance geometry won't work very well in my case. What is your better suggestion about my case? Best wishes -- 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 tutorial
On 11/10/13 9:14 AM, shahab shariati wrote: Dear Justin Very thanks for your reply. What you described earlier should not be attempted with distance geometry. It won't work very well. The use of restraints is almost NEVER necessary, especially in the case where the reference group is much more massive than the pulling group. I want to calculate Potential of mean force as a function of the distance between the centers of mass of drug and the lipid bilayer. You said distance geometry won't work very well in my case. What is your better suggestion about my case? http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/05a_pull_tips.html pull_geometry = position -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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 tutorial
Daer Justin I studied your tutorial (Umbrella Sampling). It is very beneficial for me. The system you considered was the dissociation of a single peptide from the growing end of an protofibril. You considered following parameters: Chain_B: reference group for pulling. Chain_A: group to which pulling force is applied. pulling direction was Z. you placed the center of mass of the protofibril at (3.280, 2.181, 2.4775) in a box of dimensions 6.560 x 4.362 x 12 by editconf: editconf -f complex.gro -o newbox.gro -center 3.280 2.181 2.4775 -box 6.560 4.362 12. I have a question: You said pull distance must always be less than one-half the length of the box vector along which the pulling is being conducted.You pulled a total distance of 5.0 nm in a 12.0-nm box, to avoid the complications described above. Why did you used 2.4775? I think 5.0 is true. Please give me more explanation. How did you obtained this value? Best wishes -- 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 tutorial
On 11/9/13 8:22 AM, shahab shariati wrote: Daer Justin I studied your tutorial (Umbrella Sampling). It is very beneficial for me. The system you considered was the dissociation of a single peptide from the growing end of an protofibril. You considered following parameters: Chain_B: reference group for pulling. Chain_A: group to which pulling force is applied. pulling direction was Z. you placed the center of mass of the protofibril at (3.280, 2.181, 2.4775) in a box of dimensions 6.560 x 4.362 x 12 by editconf: editconf -f complex.gro -o newbox.gro -center 3.280 2.181 2.4775 -box 6.560 4.362 12. I have a question: You said pull distance must always be less than one-half the length of the box vector along which the pulling is being conducted.You pulled a total distance of 5.0 nm in a 12.0-nm box, to avoid the complications described above. Why did you used 2.4775? I think 5.0 is true. Please give me more explanation. How did you obtained this value? I knew I needed a rectangular box, given the intrinsic geometry of the protein complex and the manner in which I was pulling, so I started by building a cubic box around the pentamer that satisfied normal minimum image convention criteria based on my cutoffs. I noted its dimensions and extended the box by 5.0 nm along z, then added a bit of padding space, because the COM distance itself is not the only factor that is important; I had to simultaneously account for the fact that I was unfolding a peptide along the reaction coordinate. So I added a bit more space for good measure to avoid spurious PBC interactions at the end of the reaction coordinate. It's all fairly empirical, determined stepwise by accounting for the important features of the system. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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 tutorial
Dear Justin Thanks for your explanation. My system contains lipid bilayer + drug + water molecules. I want to calculate Potential of mean force as a function of the distance between the centers of mass of drug and the lipid bilayer. Box vector along which the pulling is being conducted is Z. 1) Are these issues true about my system? lipid bilayer = reference group for pulling. drug molecule = group to which pulling force is applied. Then, should I use position restraining on the lipid bilayer? 2) The system you considered was the dissociation of a single peptide from the growing end of an protofibril. So, in your summary_distances.dat, distance between chain A and chain B was increased. But, I want to consider translocation of the drug molecule from water into the lipid bilayer. On the other hand, I want to consider approaching drug molecule to lipid bilayer. So, in my summary_distances.dat, distance between drug molecule and lipid bilayer will be decrease. My mean is that my case is contrary to your case. Nonetheless, should I use exactly Pull code section of your md_pull.mdp file? Best wishes -- 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 tutorial
On 11/9/13 9:38 AM, shahab shariati wrote: Dear Justin Thanks for your explanation. My system contains lipid bilayer + drug + water molecules. I want to calculate Potential of mean force as a function of the distance between the centers of mass of drug and the lipid bilayer. Box vector along which the pulling is being conducted is Z. 1) Are these issues true about my system? lipid bilayer = reference group for pulling. drug molecule = group to which pulling force is applied. Then, should I use position restraining on the lipid bilayer? I see no reason for that. The use of position restraints represents a special case, the logic for which is described in our paper. Please do not extrapolate too literally from my tutorial to your system. 2) The system you considered was the dissociation of a single peptide from the growing end of an protofibril. So, in your summary_distances.dat, distance between chain A and chain B was increased. But, I want to consider translocation of the drug molecule from water into the lipid bilayer. On the other hand, I want to consider approaching drug molecule to lipid bilayer. So, in my summary_distances.dat, distance between drug molecule and lipid bilayer will be decrease. ...and then increase, if you want to study the partitioning across the membrane. My mean is that my case is contrary to your case. Nonetheless, should I use exactly Pull code section of your md_pull.mdp file? Absolutely not! Please refer to the advanced section of the tutorial. The settings you will need will be very different from the tutorial, which represents the simplest possible case of pulling. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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 tutorial
Dear Justin, About Umbrella sampling tutorial, would you please let me know why you created an index file contains of chain A and chain B? Also, what's the meaning of 19 and 20 created by a text editoras groups.txt file? I can not understand this. Thanks in advance. Sincerely, Shima -- 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 tutorial
On 4/29/13 6:42 AM, Shima Arasteh wrote: Dear Justin, About Umbrella sampling tutorial, would you please let me know why you created an index file contains of chain A and chain B? Also, what's the meaning of 19 and 20 created by a text editoras groups.txt file? I can not understand this. Please read http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/05_pull.html again. It answers both of those questions. For further explanation about the use of groups.txt, please read http://www.gromacs.org/Documentation/How-tos/Using_Commands_in_Scripts. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * 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 tutorial quastion
Hello, According to Justin's tutorial on umbrella sampling, link: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/06_umbrella.html could anyone explain, if the molecules are restrained in any way in the umbrella sampling part? What I mean, is when we pull molecule A from molecule B, we restrain B to that it does not follow A (by adding pos_res section in .itp file). In my particular case, I pull asparagin asid (ASP) from lisyne (LYS), so I have got two .itp files for both molecules. Restraining LYS worked well for generating configurations, but failed for umbrella sampling. My molecules (including LYS which was restrained) were flying randomly all over the box which resulted in incorrect PMF courve. So, during umbrella sampling, shall both the molecules be restrained, none, or only one of them? Why? thanks in advance, Przemek -- 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 tutorial quastion
przemek bartha wrote: Hello, According to Justin's tutorial on umbrella sampling, link: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/06_umbrella.html could anyone explain, if the molecules are restrained in any way in the umbrella sampling part? The umbrella potential itself is a restraint. What I mean, is when we pull molecule A from molecule B, we restrain B to that it does not follow A (by adding pos_res section in .itp file). The position restraint used during steered MD in the tutorial is different from the umbrella restraint, practically and conceptually. Please refer to the associated paper for the underlying reason. Position restraints are not necessarily required for any umbrella sampling process. In my particular case, I pull asparagin asid (ASP) from lisyne (LYS), so I have got two .itp files for both molecules. Restraining LYS worked well for generating configurations, but failed for umbrella sampling. My molecules (including LYS which was restrained) were flying randomly all over the box which resulted in incorrect PMF courve. This sounds like more of a problem related to system construction rather than anything related to restraints, i.e. you have one molecule at the edge of a periodic boundary. So, during umbrella sampling, shall both the molecules be restrained, none, or only one of them? Why? In principle, no restraint aside from the umbrella potential itself is required to carry out umbrella sampling. -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 tutorial quastion
As I know, it is not necessary to restrain neither reference nor pulled group. When you apply pulling force, it means you have restrained both of them. Dariush On Mon, Jan 9, 2012 at 4:15 PM, przemek bartha przemekbar...@gmail.comwrote: Hello, According to Justin's tutorial on umbrella sampling, link: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/06_umbrella.html could anyone explain, if the molecules are restrained in any way in the umbrella sampling part? What I mean, is when we pull molecule A from molecule B, we restrain B to that it does not follow A (by adding pos_res section in .itp file). In my particular case, I pull asparagin asid (ASP) from lisyne (LYS), so I have got two .itp files for both molecules. Restraining LYS worked well for generating configurations, but failed for umbrella sampling. My molecules (including LYS which was restrained) were flying randomly all over the box which resulted in incorrect PMF courve. So, during umbrella sampling, shall both the molecules be restrained, none, or only one of them? Why? thanks in advance, Przemek -- 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 -- Kind Regards, Dariush Mohammadyani Department of Structural Biology University of Pittsburgh School of Medicine Biomedical Science Tower 3 3501 Fifth Avenue Pittsburgh, PA 15261 USA -- 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 tutorial
Hey Gmx Users, I went through Justin tutorial of umbrella sampling with spacing of 0.2 nm: Time COM distance 0 - 0.5 208 - 0.7 218 - 0.92 225 - 1.119 231 - 1.41 235 - 1.61 239 - 1.81 246 - 2.09 253 - 2.3 261 - 2.51 268 - 2.71 276 - 2.91 289 - 3.11 307 - 3.3 325 - 3.5 348 - 3.7 359 - 3.93 371 - 4.1 388 - 4.3 412 - 4.51 423 - 4.7 450 - 4.92 454 - 5 Together 22 windows. I obtained delatG= -37 kcal/mol Do you have any clue why is that so far away from the value from tutorial of -50.5 kcal./mol? Thank you, Steven -- 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 tutorial
Steven Neumann wrote: Hey Gmx Users, I went through Justin tutorial of umbrella sampling with spacing of 0.2 nm: Time COM distance 0 - 0.5 208 - 0.7 218 - 0.92 225 - 1.119 231 - 1.41 235 - 1.61 239 - 1.81 246 - 2.09 253 - 2.3 261 - 2.51 268 - 2.71 276 - 2.91 289 - 3.11 307 - 3.3 325 - 3.5 348 - 3.7 359 - 3.93 371 - 4.1 388 - 4.3 412 - 4.51 423 - 4.7 450 - 4.92 454 - 5 Together 22 windows. I obtained delatG= -37 kcal/mol Do you have any clue why is that so far away from the value from tutorial of -50.5 kcal./mol? Not really. You don't have the even 0.2-nm spacing that the tutorial calls for, but I know others have reproduced the value, so it should certainly be possible. -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
