Re: [gmx-users] PMF of ligand transport
Hi, I tried to calculate PMF for the ligand transport using pull_geometry=position. Let me explain you what I did so far, I picked a small collection of backbone atoms nearly from the centre of the channel.My SMD was displacing the ligand from extracellular to intracellular. I checked the pullx file for getting the window spacing (pull_init ). Initial structure is at =7.61 Centre of the channel(reference) =8.20 Last displacement is at =8.91 Therfore I selected pul_init as 0.6, 0.5, 0.4 ,0-0.4,-0.5,-0.6 For example, the first frame(at 7.61) was sampled using the following parameters, pull = umbrella pull_geometry= position pull_dim = N N Y pull_start = no pull_nstxout = 10 pull_nstfout = 10 pull_ngroups = 1 pull_group0 = U_ref pull_pbcatom0= 0 pull_group1 = r_C1 pull_pbcatom1= 0pull_k1 = pull_init1 = 0 0 0.6 pull_k1 = 1000 pull_rate1 = 0 pull_vec1= 0 0 0 The problem is that the ligand undergoes a displacement to wrong direction during sampling. My idea was pull_k1 = 1000 is the force to keep ligand in one place where it get sampled? Is there anything wrong that I am doing? any suggestions will be appreciated. -Aswathy On Tue, May 11, 2010 at 11:15 AM, Aswathy ammasa...@gmail.com wrote: Hi Chris, Thank you very much for your detailed mail. Now I have a doubt on this pull_init parameter. i read your previous posts regarding this, but still have a confusion. My query is that for each configuration when I run umbrella sampling, will this pull_init value needs to change?(I suppose so, if its true how?) When it should be negative and positive? Could you please explain this. Thanks for your valuable time Thanks Regards, Aswathy On Mon, May 10, 2010 at 9:55 PM, Chris Neale chris.ne...@utoronto.cawrote: Pick a small collection of backbone atoms near the center of your channel and use them as your reference group. Overcome the sign problem by optimal selection of pull options (see below). pull_pbcatom values should not be important if you select your groups as I suggest -- otherwise be sure to understand how they work. ; COM PULLING pull = umbrella pull_geometry= position pull_dim = N N Y pull_start = no pull_nstxout = 250 pull_nstfout = 250 pull_ngroups = 1 pull_group0 = MY_SELECTION_OF_BACKBONE_ATOMS pull_pbcatom0= 0 pull_group1 = LIGAND pull_pbcatom1= 0 pull_init1 = 0 0 THISDIST pull_rate1 = 0 pull_k1 = 500.0 pull_vec1= 0 0 0 Chris. -- original message -- I think Justin meant that you have various positions of the ligand in the channel (from the SMD), so you don't need to make a new run to determine new positions in the channel. You need only new umbrella sampling simulations. Yep, the movement of the particle will also matter, because if the particle moves much on the z-axis, the distance between the particle and the ligand will change. So you would want the particle fixed relative to the channel. Two ideas: Place the particle above the entrance of the channel. Pick three atoms from the entrance of the channel and determine the distance between the atoms and the particle. Then use distance_restraints or constraints with a 'bondlength' equal to the measured distance. If everything goes right the particle would stay where you placed it, since it does not interact with the enviroment it should not really influence your simulation (only through the constraints or distance_restraints). I don't now how big your system is, but it would probably be a good idea to make a short test simulation, to look if the particle changes the system behavior. But it's only an idea, i hope other people comment it. Greetings Thomas -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Aswathy -- Aswathy -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] ions
hi gromacs users how can i add multiple type of ions to my solvent. i tried it with genion but it accepts only one type of ion. thanks -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] RE: .rtp libraries lipids...
Dear All, This is a follow up on a post last week. I was trying to find pre-made .rtp libraries to add on for membrane lipids (other than DOPC, etc...). My critique was the complexity of membrane lipids means for most real processes we need to have a synthetic membrane (s) that reflect real life more acurattly, but figured people do not want to share their libraries for obvious reasons, etc... In any case I could not find the exact review article, which lists similar figures and tables as below for most cells, and membranes within cells, but it is similar to this article... Lipid Composition of Cultured Murine Keratinocytes Kathi C Madison, Philip W Wertz, John S Strauss and Donald T Downing CHeers Stephan Watkins -- GMX.ch - Schweizer FreeMail-Dienst mit über 800.000 Mitgliedern E-Mail mehr! Kostenlos: http://portal.gmx.net/de/go/chfreemail -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] ions
- Original Message - From: tahereh tekieh golesan...@gmail.com Date: Monday, May 17, 2010 17:47 Subject: [gmx-users] ions To: gmx-users@gromacs.org hi gromacs users how can i add multiple type of ions to my solvent. i tried it with genion but it accepts only one type of ion. Add one lot of ions with genion. Then add another lot of ions with a second invocation of genion. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] ions
using second invocation of genion replaces new ions with the older ones if the they have same amount of ions. On Mon, May 17, 2010 at 12:23 PM, Mark Abraham mark.abra...@anu.edu.auwrote: - Original Message - From: tahereh tekieh golesan...@gmail.com Date: Monday, May 17, 2010 17:47 Subject: [gmx-users] ions To: gmx-users@gromacs.org hi gromacs users how can i add multiple type of ions to my solvent. i tried it with genion but it accepts only one type of ion. Add one lot of ions with genion. Then add another lot of ions with a second invocation of genion. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] RE: .rtp libraries lipids...
On 5/17/10 9:51 AM, lloyd riggs wrote: Dear All, This is a follow up on a post last week. I was trying to find pre-made .rtp libraries to add on for membrane lipids (other than DOPC, etc...). My critique was the complexity of membrane lipids means for most real processes we need to have a synthetic membrane (s) that reflect real life more acurattly, but figured people do not want to share their libraries for obvious reasons, etc... The reason there are no such libraries is that pdb2gmx can not handle these easily, since it is made for proteins. The main problem is that such molecules do not usually have the same atom names in all coordinate files, and this is what pdb2gmx relies on. You can find lipid topologies on Peter Tieleman's website (itp files). Of course if someone would provide lots of different coordinate files and rtp files this could work in combination, but not for arbitrary lipids. In any case I could not find the exact review article, which lists similar figures and tables as below for most cells, and membranes within cells, but it is similar to this article... Lipid Composition of Cultured Murine Keratinocytes Kathi C Madison, Philip W Wertz, John S Strauss and Donald T Downing CHeers Stephan Watkins -- David. David van der Spoel, PhD, Professor of Biology Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 sp...@xray.bmc.uu.sesp...@gromacs.org http://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] RE: .rtp libraries lipids...
Hi, I am not exactly sure about your question, but for lipids and membrane composition there are several books about lipids e.g. The Lipid Handbook 'Biomembranes' by Gennis. A good source for topologies (itp-files) is: http://lipidbook.bioch.ox.ac.uk/ Best wishes Andreas -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of lloyd riggs Sent: 17 May 2010 08:52 To: gmx-users@gromacs.org Subject: [gmx-users] RE: .rtp libraries lipids... Dear All, This is a follow up on a post last week. I was trying to find pre-made .rtp libraries to add on for membrane lipids (other than DOPC, etc...). My critique was the complexity of membrane lipids means for most real processes we need to have a synthetic membrane (s) that reflect real life more acurattly, but figured people do not want to share their libraries for obvious reasons, etc... In any case I could not find the exact review article, which lists similar figures and tables as below for most cells, and membranes within cells, but it is similar to this article... Lipid Composition of Cultured Murine Keratinocytes Kathi C Madison, Philip W Wertz, John S Strauss and Donald T Downing CHeers Stephan Watkins -- GMX.ch - Schweizer FreeMail-Dienst mit über 800.000 Mitgliedern E-Mail mehr! Kostenlos: http://portal.gmx.net/de/go/chfreemail -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] ions
- Original Message - From: tahereh tekieh golesan...@gmail.com Date: Monday, May 17, 2010 18:01 Subject: Re: [gmx-users] ions To: Discussion list for GROMACS users gmx-users@gromacs.org using second invocation of genion replaces new ions with the older ones if the they have same amount of ions. That doesn't sound all that likely. What pair of genion commands do you say does that? Alternatively, use genion for A+B ions of type A, and then select B of them randomly to replace by the B ion with a text editor. (To see how those lines should look, do a separate test insertion of B with genion!) Then edit the output .gro and .top by hand to reflect the changes. You will need to make the ordering of molecules in the coordinate file match the [ molecules ] section by re-ordering the A and B ions to be contiguous chunks. Mark On Mon, May 17, 2010 at 12:23 PM, Mark Abraham mark.abra...@anu.edu.au wrote: - Original Message - From: tahereh tekieh golesan...@gmail.com Date: Monday, May 17, 2010 17:47 Subject: [gmx-users] ions To: gmx-users@gromacs.org hi gromacs users how can i add multiple type of ions to my solvent. i tried it with genion but it accepts only one type of ion. Add one lot of ions with genion. Then add another lot of ions with a second invocation of genion. Mark -- gmx-users mailing list gmx-us...@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] PMF of ligand transport
On Mon, May 17, 2010 at 12:14 PM, Aswathy ammasa...@gmail.com wrote: Hi, I tried to calculate PMF for the ligand transport using pull_geometry=position. Let me explain you what I did so far, I picked a small collection of backbone atoms nearly from the centre of the channel.My SMD was displacing the ligand from extracellular to intracellular. I checked the pullx file for getting the window spacing (pull_init ). Initial structure is at =7.61 Centre of the channel(reference) =8.20 Last displacement is at =8.91 Therfore I selected pul_init as 0.6, 0.5, 0.4 ,0-0.4,-0.5,-0.6 For example, the first frame(at 7.61) was sampled using the following parameters, pull = umbrella pull_geometry= position pull_dim = N N Y pull_start = no pull_nstxout = 10 pull_nstfout = 10 pull_ngroups = 1 pull_group0 = U_ref pull_pbcatom0= 0 pull_group1 = r_C1 pull_pbcatom1= 0 pull_init1 = 0 0 0.6 pull_k1 = 1000 pull_rate1 = 0 pull_vec1= 0 0 0 The problem is that the ligand undergoes a displacement to wrong direction during sampling. My idea was pull_k1 = 1000 is the force to keep ligand in one place where it get sampled? I want to add some more points to this. I agree that as I am using the Position , it should be displaced to the position of reference. But my worry is that, when i visualize this trajectory, within the first two or three frames, ligand get displaced. As per my u understanding, we need to sample well at the same position to get the PMF at that point.(Is it so?) in that case, the sudden drop from the initial position will cause any problem in the PMF? Is there anything wrong that I am doing? any suggestions will be appreciated. -Aswathy On Tue, May 11, 2010 at 11:15 AM, Aswathy ammasa...@gmail.com wrote: Hi Chris, Thank you very much for your detailed mail. Now I have a doubt on this pull_init parameter. i read your previous posts regarding this, but still have a confusion. My query is that for each configuration when I run umbrella sampling, will this pull_init value needs to change?(I suppose so, if its true how?) When it should be negative and positive? Could you please explain this. Thanks for your valuable time Thanks Regards, Aswathy On Mon, May 10, 2010 at 9:55 PM, Chris Neale chris.ne...@utoronto.cawrote: Pick a small collection of backbone atoms near the center of your channel and use them as your reference group. Overcome the sign problem by optimal selection of pull options (see below). pull_pbcatom values should not be important if you select your groups as I suggest -- otherwise be sure to understand how they work. ; COM PULLING pull = umbrella pull_geometry= position pull_dim = N N Y pull_start = no pull_nstxout = 250 pull_nstfout = 250 pull_ngroups = 1 pull_group0 = MY_SELECTION_OF_BACKBONE_ATOMS pull_pbcatom0= 0 pull_group1 = LIGAND pull_pbcatom1= 0 pull_init1 = 0 0 THISDIST pull_rate1 = 0 pull_k1 = 500.0 pull_vec1= 0 0 0 Chris. -- original message -- I think Justin meant that you have various positions of the ligand in the channel (from the SMD), so you don't need to make a new run to determine new positions in the channel. You need only new umbrella sampling simulations. Yep, the movement of the particle will also matter, because if the particle moves much on the z-axis, the distance between the particle and the ligand will change. So you would want the particle fixed relative to the channel. Two ideas: Place the particle above the entrance of the channel. Pick three atoms from the entrance of the channel and determine the distance between the atoms and the particle. Then use distance_restraints or constraints with a 'bondlength' equal to the measured distance. If everything goes right the particle would stay where you placed it, since it does not interact with the enviroment it should not really influence your simulation (only through the constraints or distance_restraints). I don't now how big your system is, but it would probably be a good idea to make a short test simulation, to look if the particle changes the system behavior. But it's only an idea, i hope other people comment it. Greetings Thomas -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it
[gmx-users] About wiki error
Hi, there seems two errors in the following page: http://www.gromacs.org/Documentation/Terminology/NVT say NVT is microcanonical ensemble. and http://www.gromacs.org/Documentation/Terminology/NVE say NVE is canonical ensemble. I register at wiki, but haven't authority to modify them. Can anybody fix them? Thank you! Ref: http://en.wikipedia.org/wiki/Molecular_dynamics -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] PMF of ligand transport
Aswathy wrote: On Mon, May 17, 2010 at 12:14 PM, Aswathy ammasa...@gmail.com mailto:ammasa...@gmail.com wrote: Hi, I tried to calculate PMF for the ligand transport using pull_geometry=position. Let me explain you what I did so far, I picked a small collection of backbone atoms nearly from the centre of the channel.My SMD was displacing the ligand from extracellular to intracellular. I checked the pullx file for getting the window spacing (pull_init ). Initial structure is at =7.61 Centre of the channel(reference) =8.20 Last displacement is at =8.91 Therfore I selected pul_init as 0.6, 0.5, 0.4 ,0-0.4,-0.5,-0.6 For example, the first frame(at 7.61) was sampled using the following parameters, pull = umbrella pull_geometry= position pull_dim = N N Y pull_start = no pull_nstxout = 10 pull_nstfout = 10 pull_ngroups = 1 pull_group0 = U_ref pull_pbcatom0= 0 pull_group1 = r_C1 pull_pbcatom1= 0 pull_init1 = 0 0 0.6 pull_k1 = 1000 pull_rate1 = 0 pull_vec1= 0 0 0 The problem is that the ligand undergoes a displacement to wrong direction during sampling. My idea was pull_k1 = 1000 is the force to keep ligand in one place where it get sampled? I want to add some more points to this. I agree that as I am using the Position , it should be displaced to the position of reference. But my worry is that, when i visualize this trajectory, within the first two or three frames, ligand get displaced. As per my u understanding, we need to sample well at the same position to get the PMF at that point.(Is it so?) in that case, the sudden drop from the initial position will cause any problem in the PMF? There is nothing wrong. Your ligand will move around; that's what MD does. As long as the reference distance between your ligand and bilayer remains correct there is no problem. The umbrella potential is a harmonic restraining force, allowing for some deviation in position such that the ligand about the sampling window. If there is some drastic change in position such that this reference distance is no longer conserved, then you have a problem. But certainly this is not what is happening within only a few frames. -Justin Is there anything wrong that I am doing? any suggestions will be appreciated. -Aswathy On Tue, May 11, 2010 at 11:15 AM, Aswathy ammasa...@gmail.com mailto:ammasa...@gmail.com wrote: Hi Chris, Thank you very much for your detailed mail. Now I have a doubt on this pull_init parameter. i read your previous posts regarding this, but still have a confusion. My query is that for each configuration when I run umbrella sampling, will this pull_init value needs to change?(I suppose so, if its true how?) When it should be negative and positive? Could you please explain this. Thanks for your valuable time Thanks Regards, Aswathy On Mon, May 10, 2010 at 9:55 PM, Chris Neale chris.ne...@utoronto.ca mailto:chris.ne...@utoronto.ca wrote: Pick a small collection of backbone atoms near the center of your channel and use them as your reference group. Overcome the sign problem by optimal selection of pull options (see below). pull_pbcatom values should not be important if you select your groups as I suggest -- otherwise be sure to understand how they work. ; COM PULLING pull = umbrella pull_geometry= position pull_dim = N N Y pull_start = no pull_nstxout = 250 pull_nstfout = 250 pull_ngroups = 1 pull_group0 = MY_SELECTION_OF_BACKBONE_ATOMS pull_pbcatom0= 0 pull_group1 = LIGAND pull_pbcatom1= 0 pull_init1 = 0 0 THISDIST pull_rate1 = 0 pull_k1 = 500.0 pull_vec1= 0 0 0 Chris. -- original message -- I think Justin meant that you have various positions of the ligand in the channel (from the SMD), so you don't need to make a new run to determine new positions in the channel. You need only new umbrella sampling simulations. Yep, the movement of the particle will also matter,
Re: [gmx-users] About wiki error
Cun Zhang wrote: Hi, there seems two errors in the following page: http://www.gromacs.org/Documentation/Terminology/NVT say NVT is microcanonical ensemble. and http://www.gromacs.org/Documentation/Terminology/NVE say NVE is canonical ensemble. I register at wiki, but haven't authority to modify them. Can anybody fix them? Fixed. I think you need to contact Rossen to get editing permission on the site after you've registered. -Justin Thank you! Ref: http://en.wikipedia.org/wiki/Molecular_dynamics -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] interaction parameter-polymer solution system
Dear experts, I am interested in calculation of Flory interaction parameter for ternary system of polyethylene/n-Hexane/ethylene. Flory-Huggins lattice theory for polymer solvent systems defines interaction parameter (binary) in terms of interaction energies between lattice sites. binary interaction parameter =z*delta (e)/RT z=coordination NO. which is the number of neighbors in a lattice site delta e=e12 -(e11+e22)/2 : net change in interaction energies upon mixing (polymer: polyethylene in solvent :hexane) e12 [kcal/mol] is the interaction energy between polymer and solvent (of course after mixing) e11, e22 interaction energy between identical molecules before mixing (polymer or solvent) Since we are talking about energies between lattice sites my interpretation is that only non bonded interactions should be considered among all energy terms.(vdw and electrostatics). 1- However, I dont know if I need to include electrostatics terms since the system is apolar (only hydrocarbons). Also, do LJ energy figures (or coulomb) given by g_energy refer to e11,e22.. interaction energies? 2- To calculate these interaction energies, for instance for identical molecules , Hexane, how many molecules i need to put in a simulation box. 3- Do I need to consider free energy of solvation for this type of calculation? Many thanks, Moeed -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] interaction parameter-polymer solution system
Moeed wrote: Dear experts, I am interested in calculation of Flory interaction parameter for ternary system of polyethylene/n-Hexane/ethylene. Flory-Huggins lattice theory for polymer solvent systems defines interaction parameter (binary) in terms of interaction energies between lattice sites. binary interaction parameter =z*delta (e)/RT z=coordination NO. which is the number of neighbors in a lattice site delta e=e12 -(e11+e22)/2 : net change in interaction energies upon mixing (polymer: polyethylene in solvent :hexane) e12 [kcal/mol] is the interaction energy between polymer and solvent (of course after mixing) e11, e22 interaction energy between identical molecules before mixing (polymer or solvent) Since we are talking about energies between lattice sites my interpretation is that only non bonded interactions should be considered among all energy terms.(vdw and electrostatics). 1- However, I dont know if I need to include electrostatics terms since the system is apolar (only hydrocarbons). Also, do LJ energy figures (or coulomb) given by g_energy refer to e11,e22.. interaction energies? You are still using OPLS-AA, are you not? If so, then your atoms have partial charges on them and therefore there are electrostatic interactions between your molecules. You can't ignore this term. By default, you will not get these interaction energies decomposed as you would like. You can, however, set energygrps in the .mdp file to separate out these contributions. If using PME, however, there will be a long-range term that simply cannot be decomposed, so choose your long-range electrostatics method carefully. 2- To calculate these interaction energies, for instance for identical molecules , Hexane, how many molecules i need to put in a simulation box. Enough to get convergence :) 3- Do I need to consider free energy of solvation for this type of calculation? Sorry, can't comment on this. Maybe someone else can. From the above equations, there don't seem to be any free energies involved at all, but I've got very little experience in polymers. -Justin Many thanks, Moeed -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] pressure for ambient water
Amit Choubey wrote: On Sun, May 16, 2010 at 7:41 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Amit Choubey wrote: On Sun, May 16, 2010 at 5:15 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: Amit Choubey wrote: Hi Justin, Since the density (1 gm/cc) and T (300 K) correspond to ambient condition, should not the equation of state dictate a pressure around 1 atm? If the equation of state involves temperature and pressure, yes. So if you fix the density and temperature shouldnt you land up with right pressure which we know should be 1 atm. You are not fixing (or conserving) the temperature in an NVE ensemble. That would be an NVT ensemble, employing a thermostat. I did do NVT first and then for sampling i removed the thermostat. Also as you mentioned there was not much difference b/n pressure values during NVT or NVE . The pressure value is as high as 1000 bar in both cases. Since instantaneous pressure is calculated (in part) from the kinetic energy, and since the kinetic energy is not guaranteed to be conserved, the pressure term will also fluctuate accordingly. This is correct. The pressure thus fluctuates about 20 % of the above mentioned value. http://www.gromacs.org/Documentation/Terminology/Pressure The internal energy of the system is constant in an NVE ensemble, the other terms may fluctuate as necessary such that all microstates occur with the same probability and the energy surface remains flat. I agree Also recall that an NVE ensemble represents a thermodynamically isolated system, not conducting heat or engaging in work with the surrounding system. true So any concept of external pressure and equilibrating the pressure is irrelevant. I am not trying to equilibriate the pressure. I am trying to measure the pressure. I also know that at 300 K and 1gm/cc the P should be 1 bar. Also, theoretically NVE or NVT are no different than NPT as far as measuring observables is concerned. Hence i was thinking that if you have the right volume density and temperature shouldnt you have the right pressure. I think the disconnect is arising because you're expecting a model of water to behave almost like an ideal gas. The SPC water model, under NPT conditions of 300 K and 1 bar, does not give the experimental density of water; it is actually somewhat less than 1 g/mL. So constraining the system to fit some pre-conceived notion of the volume to force the density to be right conflicts with the properties of the water model itself. SPC wants to be at a lower density, you're forcing it to be at a higher density, all while fixing the volume of the simulation cell. Sounds to me like a recipe for high pressure, since SPC wants to expand but you won't let it. So the starting configuration, assembled with the right density, has not properly equilibrated under NPT conditions, yet you are expecting it to do so when applying NVE conditions. I don't know that you'll ever be able to satisfy all of these requirements simultaneously unless you can come up with a better water model that replicates both ideal and real behavior :) -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/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: Need Help about GROMACS.
Regardless of whether or not you've received a response, please keep all correspondence on the gmx-users list. I am not a private tutor. To what post are you referring? The list is fairly high-traffic, so if it's been a long time since you posted, don't continue to wait for a response. Post a new question, expanding upon your previous problem with any new details. You're more likely to get help if you demonstrate you are trying to help yourself. You're applying opposing forces between your lipids and water? That certainly sounds like a recipe for collapse. Perhaps if you can describe (by posting to the list) what you're doing, what you're hoping to accomplish, and what your .mdp settings are, you might get some more useful advice. -Justin Archana S Achalere wrote: Dear Dr. Justin Lamkul, I apologies that I am writing directly to you the query about my simulation. As since long I have not got any response of my query posted on gmx-users. I am simulating lipid bilayer (DPPC + water) where I give equal and opposite force (along bilayer normal) on lipid and water molecules I face two problems: 1. If I remove center of mass motion of whole System then the simulation box stars suppressing along z direction (bilayer normal) and eventually simulation terminates after few thousands of time steps. 2. If I give two groups DPPC and water for center of mass motion removal, then bilayer moves along z direction (bilayer normal). Could you please give me some direction how to resolve this. Thank you. Regards, -Archana Department of Chemical Engineering, Indian Institute of Science, Bangalore, India. -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Domain decomposition error
Thanks Mark, I did play around with the -npme option a little and turns out using -npme 1 works for the system this is mdrun command I have in the script file mdrun_openmpi -nosum -dlb yes -npme 1 -cpt 40 -maxh 48 -deffnm md Thanks. Quoting Mark Abraham mark.abra...@anu.edu.au: - Original Message - From: nishap.pa...@utoronto.ca Date: Monday, May 17, 2010 10:28 Subject: Re: [gmx-users] Domain decomposition error To: gmx-users@gromacs.org Thanks Justin. But how come it worked for methanol. The system is of the same size , and all the parameters are same, so I don't understand why it won't work for ethanol. I'd guess that the greater size of ethanol in combination with constraints is running afoul of the DD minimum cell-size requirements. As you will see in reading the .log file, for your ethanol, P-LINCS requires at least 0.497nm given the initial condition of your system. DD fudges that up by a factor of 1.25 to give some flexibility. Given that minimimum size requirement, only 6 cells can result from a partition in any dimension of a 4nm x 4nm x 4nm box. You've probably artificially required DD to use 14 processors with -npme 2. That requires a 14x1x1 or 7x2x1 DD, neither of which can be consistent with the combination of your box size and constraint usage. Methanol will have a smaller constraint (see its .log file to compare), so the DD will be legal. If you'd given your full mdrun command line in your post, then I wouldn't be guessing as much... The .log file recommends a range of useful solutions for you to consider - but it makes no suggests regarding your .mdp file. Roughly speaking, the .mdp file normally describes the model physics and controls the output conditions, and the (sometimes implicit) arguments of mdrun describe the implemention of the resulting algorithm. You're requiring an impossible implementation. Simplest is to not specify -npme unless you know you need to. For efficiency, both -npme and -np less -npme need to be sufficiently composite and preferably with a high common factor of two of their factors. If you leave mdrun alone, it will guess reasonably. For example, -npme=4 giving 12 DD nodes decomposed 4x3x1 will work admirably in your case, and I bet that's what mdrun picks. Mark Quoting Justin A. Lemkul jalem...@vt.edu: nishap.pa...@utoronto.ca wrote: Hello, I got this following error when I was trying to run a simulation of ethanol-water box size 4*4*4 nm (~6530 atoms). Fatal error: There is no domain decomposition for 14 nodes that is compatible with the given box and a minimum cell size of 0.62175 nm Change the number of nodes or mdrun option -rcon or -dds or your LINCS settings Look in the log file for details on the domain decomposition. I looked into my log file and this is what I got: Initializing Domain Decomposition on 16 nodes Dynamic load balancing: yes Will sort the charge groups at every domain (re)decomposition Initial maximum inter charge-group distances: two-body bonded interactions: 0.234 nm, LJ-14, atoms 1 9 multi-body bonded interactions: 0.234 nm, Angle, atoms 2 5 Minimum cell size due to bonded interactions: 0.257 nm Maximum distance for 5 constraints, at 120 deg. angles, all- trans: 0.497 nm Estimated maximum distance required for P-LINCS: 0.497 nm This distance will limit the DD cell size, you can override this with -rcon Guess for relative PME load: 0.13 Will use 14 particle-particle and 2 PME only nodes This is a guess, check the performance at the end of the log file Using 2 separate PME nodes Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25 Optimizing the DD grid for 14 cells with a minimum initial size of 0.622 nm The maximum allowed number of cells is: X 6 Y 6 Z 6 I am using the same .mdp file that I used for methanol, and it is working fine, I don't understand why it's giving me problem for ethanol. I am running my simulation on 2 nodes. Not according to the log file messages. You're running on 16 nodes, with 14 for PP and 2 for PME. Your system is of insufficient size to be divided over this many PP nodes. Check the list archive for tips, or simply use less nodes for the calculation. There is also information in the manual about all of the settings that are mentionedin the log file. -Justin Suggestions? Thanks -Nisha P -- 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/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to
[gmx-users] Total energy -decomposed terms
Dear Justin, Thanks so much for your comments. As for my question below: * ... Also, do LJ energy figures (or coulomb) given by g_energy refer to e11,e22.. interaction energies? Justin: By default, you will not get these interaction energies decomposed as you would like. You can, however, set energygrps in the .mdp file to separate out these contributions. If using PME, however, there will be a long-range term that simply cannot be decomposed, so choose your long-range electrostatics method carefully. I go ahead and read about energy groups but I have a question here. So what are the energy terms like LJ or coulomb one gets from g_energy. Are they not the decomposed terms from total energy of system? Can I not take for instance LJ energy values which are coming from a specific NO. of molecuels in simulation box and calculate interaction energies for pairs or mol number of molecules? Thank you for you help :) Moeed -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Total energy -decomposed terms
Moeed wrote: Dear Justin, Thanks so much for your comments. As for my question below: * ... Also, do LJ energy figures (or coulomb) given by g_energy refer to e11,e22.. interaction energies? Justin: By default, you will not get these interaction energies decomposed as you would like. You can, however, set energygrps in the .mdp file to separate out these contributions. If using PME, however, there will be a long-range term that simply cannot be decomposed, so choose your long-range electrostatics method carefully. I go ahead and read about energy groups but I have a question here. So what are the energy terms like LJ or coulomb one gets from g_energy. Are they not the decomposed terms from total energy of system? Can I not The default terms are the total LJ and Coulombic energy terms for the system. That could include both intra- and intermolecular terms. If you want the LJ and Coulombic energy between molecules A and B, you have to set: energygrps = A B in the .mdp file. Then you will get LJ and Coulombic terms for the interactions between these two molecule types, as well as A-A and B-B terms. take for instance LJ energy values which are coming from a specific NO. of molecuels in simulation box and calculate interaction energies for pairs or mol number of molecules? Not easily. You will still have intramolecular terms that are not covered by the 1-4 interactions. For example, if the two ends of your molecule interact with one another, this interaction will contribute to your nonbonded energies. You could do your simulation, then use mdrun -rerun with a new topology that defines all possible intramolecular exclusions in order to save only intermolecular energy contributions. Doing a simulation like this would be meaningless, of course, but you can rerun the simulation to break down the energies (that's usually what mdrun -rerun is used for). -Justin Thank you for you help :) Moeed -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Gromacs test sets
Hi everyone, I have just installed Gromacs (version 4.0.7), run the test sets (gmxtest-4.0.4) and got few failures. I looked at the relevant 'checkpot.out' and 'checkvir.out' files as suggested in previous messages. For the 'complex' tests I got no differences in the 'checkpot.out', only in the 'checkvir.out'. Some of the differences in 'checkvir.out' are quite large (see below example for water). For the 'kernel' tests I get differences both in 'checkpot.out' and in 'checkvir.out' and the differences are significant (see below example for kernel020). - Should I check any other files? - What should I do when the differences are significant? (I just installed gromacs with no errors) Thanks for your help, Efrat ___ complex/water/checkpot.out: There are 31 terms in the energy files There are 3 terms to compare in the energy files Files read succesfully _ complex/water/checkvir.out: Pressure (bar) step 50: 46893.3, step 50:44899 Vir-XX step 50: -6211.69, step 50: -6371.98 Vir-XY step 50: -2423.21, step 50: -1880.85 Vir-XZ step 50: 667.327, step 50: 381.986 Vir-YX step 50: -2422.22, step 50: -1880.17 Vir-YY step 50: -3194.86, step 50: -2649.86 Vir-YZ step 50: -2208.7, step 50: -2616.43 Vir-ZX step 50: 667.878, step 50: 382.404 Vir-ZY step 50: -2207.77, step 50: -2616.81 Vir-ZZ step 50: -1482.41, step 50: -752.677 _ _ kernel/kernel020/checkpot.out: LJ-14step 0: -63.1209, step 0: 6.50742 Potentialstep 0: -321.601, step 0: -251.972 _ _ kernel/kernel020/checkvir.out: LJ-14step 0: -63.1209, step 0: 6.50742 Potentialstep 0: -321.601, step 0: -251.972 Kinetic En. step 0: 15.0135, step 0: 29.0739 Total Energy step 0: -306.588, step 0: -222.898 Temperature step 0: 1.93226, step 0: 3.74185 Pressure (bar) step 0: -3095.37, step 0: -2497.79 Vir-XX step 0: 1127.45, step 0: 1075.85 Vir-XY step 0:63.524, step 0: 21.7761 Vir-XZ step 0: -264.813, step 0: -260.354 Vir-YX step 0: 63.5241, step 0: 21.777 Vir-YY step 0: 803.252, step 0: 581.702 Vir-ZX step 0: -264.813, step 0: -260.354 Vir-ZZ step 0: 321.207, step 0: 176.573 __-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] minimizing ligand only
Dear gmx-users, is it possible to minimize a ligand in vacuo, not inserted in a protein, using GROMACS? I tried to do it using the topology file created by PRODRG server and skipping the pdb2gmx, editconf, genbox steps, but GROMACS gave me an error indicating that it does not recognize the moleculetype. The command I used was: grompp -f em.mdp -c lig.pdb -o ligmin.tpr -o ligtopol_by_PRODRG.top I made two attempts: first, I used the .itp file directly coming from PRODRG, second, I modified this file by adding the missing infos on my ligand under the different parts [ molecules ], [ systems] and so on. But I was not able to force Gromacs recognizing my molecule. Obviously, my ligand is not a peptide, but is a small molecule. I searched for some hints in the gmx-users archive and found this message: http://lists.gromacs.org/pipermail/gmx-users/2008-October/037164.html but it seems to me that it does not answer to my problem. If I follow the Kerrigan's tutorial, it indicates how to create a topology for the ligand, but not how to minimize it in the absence of the protein. Could you give me a more clear explanation? Sorry if the request seems to be trivial, but I really can't understand what to do. Many thanks in advance and best regards Anna __ Anna Marabotti, Ph.D. Laboratory of Bioinformatics and Computational Biology Institute of Food Science - CNR Via Roma, 64 83100 Avellino Phone: +39 0825 299651 Fax: +39 0825 781585 E-mail: amarabo...@isa.cnr.it Skype account: annam1972 Web site: http://bioinformatica.isa.cnr.it/anna/anna.htm If you think you're too small to make a change, try sleeping with a mosquito -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Gromacs test sets
Efrat Noy wrote: Hi everyone, I have just installed Gromacs (version 4.0.7), run the test sets (gmxtest-4.0.4) and got few failures. I looked at the relevant 'checkpot.out' and 'checkvir.out' files as suggested in previous messages. For the 'complex' tests I got no differences in the 'checkpot.out', only in the 'checkvir.out'. Some of the differences in 'checkvir.out' are quite large (see below example for water). For the 'kernel' tests I get differences both in 'checkpot.out' and in 'checkvir.out' and the differences are significant (see below example for kernel020). - Should I check any other files? - What should I do when the differences are significant? (I just installed gromacs with no errors) The test set is largely meaningless. Please see the first few sentences here: http://www.gromacs.org/index.php?title=Download_%26_Installation/Test-Set -Justin Thanks for your help, Efrat ___ complex/water/checkpot.out: There are 31 terms in the energy files There are 3 terms to compare in the energy files Files read succesfully _ complex/water/checkvir.out: Pressure (bar) step 50: 46893.3, step 50:44899 Vir-XX step 50: -6211.69, step 50: -6371.98 Vir-XY step 50: -2423.21, step 50: -1880.85 Vir-XZ step 50: 667.327, step 50: 381.986 Vir-YX step 50: -2422.22, step 50: -1880.17 Vir-YY step 50: -3194.86, step 50: -2649.86 Vir-YZ step 50: -2208.7, step 50: -2616.43 Vir-ZX step 50: 667.878, step 50: 382.404 Vir-ZY step 50: -2207.77, step 50: -2616.81 Vir-ZZ step 50: -1482.41, step 50: -752.677 _ _ kernel/kernel020/checkpot.out: LJ-14step 0: -63.1209, step 0: 6.50742 Potentialstep 0: -321.601, step 0: -251.972 _ _ kernel/kernel020/checkvir.out: LJ-14step 0: -63.1209, step 0: 6.50742 Potentialstep 0: -321.601, step 0: -251.972 Kinetic En. step 0: 15.0135, step 0: 29.0739 Total Energy step 0: -306.588, step 0: -222.898 Temperature step 0: 1.93226, step 0: 3.74185 Pressure (bar) step 0: -3095.37, step 0: -2497.79 Vir-XX step 0: 1127.45, step 0: 1075.85 Vir-XY step 0:63.524, step 0: 21.7761 Vir-XZ step 0: -264.813, step 0: -260.354 Vir-YX step 0: 63.5241, step 0: 21.777 Vir-YY step 0: 803.252, step 0: 581.702 Vir-ZX step 0: -264.813, step 0: -260.354 Vir-ZZ step 0: 321.207, step 0: 176.573 __ -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] minimizing ligand only
Anna Marabotti wrote: Dear gmx-users, is it possible to minimize a ligand in vacuo, not inserted in a protein, using GROMACS? I tried to do it using the topology file created by PRODRG server and skipping the pdb2gmx, editconf, genbox steps, but GROMACS gave me an error indicating that it does not recognize the moleculetype. The command I used was: grompp -f em.mdp -c lig.pdb -o ligmin.tpr -o ligtopol_by_PRODRG.top I made two attempts: first, I used the .itp file directly coming from PRODRG, second, I modified this file by adding the missing infos on my ligand under the different parts [ molecules ], [ systems] and so on. But I was not able to force Gromacs recognizing my molecule. Obviously, my ligand is not a peptide, but is a small molecule. I searched for some hints in the gmx-users archive and found this message: http://lists.gromacs.org/pipermail/gmx-users/2008-October/037164.html but it seems to me that it does not answer to my problem. If I follow the Kerrigan's tutorial, it indicates how to create a topology for the ligand, but not how to minimize it in the absence of the protein. Could you give me a more clear explanation? Sorry if the request seems to be trivial, but I really can't understand what to do. You just need to create a proper .top file from the .itp file. There is very little to do in order to make this change: http://www.gromacs.org/Documentation/File_Formats/.itp_File If you need further help, please post the actual error message and your topology. On a separate note, if you're using an unedited PRODRG topology, the charges and charge groups (at face value) are often unsatisfactory, so do proceed carefully... -Justin Many thanks in advance and best regards Anna __ Anna Marabotti, Ph.D. Laboratory of Bioinformatics and Computational Biology Institute of Food Science - CNR Via Roma, 64 83100 Avellino Phone: +39 0825 299651 Fax: +39 0825 781585 E-mail: amarabo...@isa.cnr.it mailto:amarabo...@isa.cnr.it Skype account: annam1972 Web site: http://bioinformatica.isa.cnr.it/anna/anna.htm If you think you're too small to make a change, try sleeping with a mosquito -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] pressure for ambient water
On Mon, May 17, 2010 at 6:45 AM, Justin A. Lemkul jalem...@vt.edu wrote: Amit Choubey wrote: On Sun, May 16, 2010 at 7:41 PM, Justin A. Lemkul jalem...@vt.edumailto: jalem...@vt.edu wrote: Amit Choubey wrote: On Sun, May 16, 2010 at 5:15 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: Amit Choubey wrote: Hi Justin, Since the density (1 gm/cc) and T (300 K) correspond to ambient condition, should not the equation of state dictate a pressure around 1 atm? If the equation of state involves temperature and pressure, yes. So if you fix the density and temperature shouldnt you land up with right pressure which we know should be 1 atm. You are not fixing (or conserving) the temperature in an NVE ensemble. That would be an NVT ensemble, employing a thermostat. I did do NVT first and then for sampling i removed the thermostat. Also as you mentioned there was not much difference b/n pressure values during NVT or NVE . The pressure value is as high as 1000 bar in both cases. Since instantaneous pressure is calculated (in part) from the kinetic energy, and since the kinetic energy is not guaranteed to be conserved, the pressure term will also fluctuate accordingly. This is correct. The pressure thus fluctuates about 20 % of the above mentioned value. http://www.gromacs.org/Documentation/Terminology/Pressure The internal energy of the system is constant in an NVE ensemble, the other terms may fluctuate as necessary such that all microstates occur with the same probability and the energy surface remains flat. I agree Also recall that an NVE ensemble represents a thermodynamically isolated system, not conducting heat or engaging in work with the surrounding system. true So any concept of external pressure and equilibrating the pressure is irrelevant. I am not trying to equilibriate the pressure. I am trying to measure the pressure. I also know that at 300 K and 1gm/cc the P should be 1 bar. Also, theoretically NVE or NVT are no different than NPT as far as measuring observables is concerned. Hence i was thinking that if you have the right volume density and temperature shouldnt you have the right pressure. I think the disconnect is arising because you're expecting a model of water to behave almost like an ideal gas. The SPC water model, under NPT conditions of 300 K and 1 bar, does not give the experimental density of water; it is actually somewhat less than 1 g/mL. So constraining the system to fit some pre-conceived notion of the volume to force the density to be right conflicts with the properties of the water model itself. SPC wants to be at a lower density, you're forcing it to be at a higher density, all while fixing the volume of the simulation cell. Sounds to me like a recipe for high pressure, since SPC wants to expand but you won't let it. So the starting configuration, assembled with the right density, has not properly equilibrated under NPT conditions, yet you are expecting it to do so when applying NVE conditions. I don't know that you'll ever be able to satisfy all of these requirements simultaneously unless you can come up with a better water model that replicates both ideal and real behavior :) yes model is an issue too. I was just concerned about 3 orders of magnitude of difference in calculation of pressure. Thank you for the answering. amit -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/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] OPLS-AA/L force field
Dear Users, I have one question about Drug-Enzyme Complex,Similar to tutorial If I want to use GROMOS96 43a1, I can use Prodrg Beta version for drug but If I want to use OPLS-AA/L all-atom force field I can use Prodrg Beta version server too, or not?If I can't use this server, how can I make .gro file and .itp file for drug that remove from initial .pdb file? Thank you for your help _ Hotmail: Powerful Free email with security by Microsoft. https://signup.live.com/signup.aspx?id=60969-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] OPLS-AA/L force field
you zou wrote: Dear Users, I have one question about Drug-Enzyme Complex,Similar to tutorial If I want to use GROMOS96 43a1, I can use Prodrg Beta version for drug but If I want to use OPLS-AA/L all-atom force field I can use Prodrg Beta version server too, or not? No. You can't use two different force fields in one simulation system. If I can't use this server, how can I make .gro file and .itp file for drug that remove from initial .pdb file? There are several programs in the User Contributions from the website, x2top (which is distributed with Gromacs), or you can build the topology by hand. No matter what you choose, you need a thorough understanding of the mechanics of your chosen force field, methods of validation, and of course Chapter 5 in the Gromacs manual. http://www.gromacs.org/Documentation/How-tos/Parameterization -Justin Thank you for your help Hotmail: Powerful Free email with security by Microsoft. Get it now. https://signup.live.com/signup.aspx?id=60969 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] How to add an user-defined external potential
Hi, I am planning to add an external harmonic potential along z direction of a system : i.e U(z)= 0.5*K*z(**2) I was wondering if I can get an help on how to add an user-defined external potential like this in gromacs ? Thanks Sanku -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] g_sdf : error
Hello, I am trying to run g_sdf for sovlation for glucose in ionic liquids. I am trying to find distribution of anion around glucose. g_sdf -f 3.trr -n glu-emi-cl-128-no.ndx -s -mode 1 3.tpr -o sdf.plt -r First three group I selected from the same residue (Glucose). Forth grouup I selected from as anion (Anion residue ). I am geting following error. Fatal error: For single particle SDF, all reference groupsmust have the same size. Thanks Nilesh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] g_sdf : error
g_sdf -f 3.trr -n glu-emi-cl-128-no.ndx -s -mode 1 3.tpr -o sdf.plt -r Is that the exact command line you used? If so, doubt it would actually work, since it should be: g_sdf -f 3.trr -n glu-emi-cl-128-no.ndx -s 3.tpr -mode 1 -o sdf.plt -r Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When the only tool you own is a hammer, every problem begins to resemble a nail. -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users- boun...@gromacs.org] On Behalf Of Nilesh Dhumal Sent: Tuesday, 18 May 2010 5:55 AM To: gmx-users@gromacs.org Subject: [gmx-users] g_sdf : error Hello, I am trying to run g_sdf for sovlation for glucose in ionic liquids. I am trying to find distribution of anion around glucose. g_sdf -f 3.trr -n glu-emi-cl-128-no.ndx -s -mode 1 3.tpr -o sdf.plt -r First three group I selected from the same residue (Glucose). Forth grouup I selected from as anion (Anion residue ). I am geting following error. Fatal error: For single particle SDF, all reference groupsmust have the same size. Thanks Nilesh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] g_sdf : error
hey Sorry for typing mistake. I used ths command. g_sdf -f 3.trr -n glu-emi-cl-128-no.ndx -s 3.tpr -mode 1 -o sdf.plt -r Nilesh On Mon, May 17, 2010 6:37 pm, Dallas B. Warren wrote: g_sdf -f 3.trr -n glu-emi-cl-128-no.ndx -s -mode 1 3.tpr -o sdf.plt -r Is that the exact command line you used? If so, doubt it would actually work, since it should be: g_sdf -f 3.trr -n glu-emi-cl-128-no.ndx -s 3.tpr -mode 1 -o sdf.plt -r Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When the only tool you own is a hammer, every problem begins to resemble a nail. -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users- boun...@gromacs.org] On Behalf Of Nilesh Dhumal Sent: Tuesday, 18 May 2010 5:55 AM To: gmx-users@gromacs.org Subject: [gmx-users] g_sdf : error Hello, I am trying to run g_sdf for sovlation for glucose in ionic liquids. I am trying to find distribution of anion around glucose. g_sdf -f 3.trr -n glu-emi-cl-128-no.ndx -s -mode 1 3.tpr -o sdf.plt -r First three group I selected from the same residue (Glucose). Forth grouup I selected from as anion (Anion residue ). I am geting following error. Fatal error: For single particle SDF, all reference groupsmust have the same size. Thanks Nilesh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] g_sdf : error
Can you copy and paste into here what you see between: Select a reference group and 1 group And Select a group: When you run the script. Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When the only tool you own is a hammer, every problem begins to resemble a nail. -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users- boun...@gromacs.org] On Behalf Of Nilesh Dhumal Sent: Tuesday, 18 May 2010 9:29 AM To: Discussion list for GROMACS users Subject: RE: [gmx-users] g_sdf : error hey Sorry for typing mistake. I used ths command. g_sdf -f 3.trr -n glu-emi-cl-128-no.ndx -s 3.tpr -mode 1 -o sdf.plt -r Nilesh On Mon, May 17, 2010 6:37 pm, Dallas B. Warren wrote: g_sdf -f 3.trr -n glu-emi-cl-128-no.ndx -s -mode 1 3.tpr -o sdf.plt -r Is that the exact command line you used? If so, doubt it would actually work, since it should be: g_sdf -f 3.trr -n glu-emi-cl-128-no.ndx -s 3.tpr -mode 1 -o sdf.plt - r Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When the only tool you own is a hammer, every problem begins to resemble a nail. -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users- boun...@gromacs.org] On Behalf Of Nilesh Dhumal Sent: Tuesday, 18 May 2010 5:55 AM To: gmx-users@gromacs.org Subject: [gmx-users] g_sdf : error Hello, I am trying to run g_sdf for sovlation for glucose in ionic liquids. I am trying to find distribution of anion around glucose. g_sdf -f 3.trr -n glu-emi-cl-128-no.ndx -s -mode 1 3.tpr -o sdf.plt -r First three group I selected from the same residue (Glucose). Forth grouup I selected from as anion (Anion residue ). I am geting following error. Fatal error: For single particle SDF, all reference groupsmust have the same size. Thanks Nilesh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] g_sdf : error
Here are details. the first three groups from GUL residue and the last in cation (residue) Group 0 ( System) has 2584 elements Group 1 ( Protein) has 2456 elements Group 2 ( Protein-H) has 1036 elements Group 3 ( C-alpha) has 0 elements Group 4 (Backbone) has 128 elements Group 5 ( MainChain) has 129 elements Group 6 (MainChain+Cb) has 129 elements Group 7 ( MainChain+H) has 129 elements Group 8 ( SideChain) has 2327 elements Group 9 ( SideChain-H) has 907 elements Group10 ( Prot-Masses) has 2456 elements Group11 ( Non-Protein) has 128 elements Group12 ( CL) has 128 elements Group13 ( Other) has 128 elements Group14 ( GUL) has24 elements Group15 ( O) has 1 elements Group16 ( C2) has 129 elements Group17 ( C3) has 1 elements Group18 ( C4) has 129 elements Group19 ( C5) has 1 elements Group20 ( C6) has 129 elements -- -- Group39 ( EMI) has 2432 elements Group40 ( C) has 128 elements - - Group58 ( H19) has 128 elements Group59 ( CL) has 128 elements Group60 ( CL) has 128 elements Select a group: 16 Selected 16: 'C2' Select a group: 17 Selected 17: 'C3' Select a group: 18 Selected 18: 'C4' Select a group: 39 Selected 39: 'EMI' trn version: GMX_trn_file (single precision) Reading frame 0 time0.000 --- Program g_sdf, VERSION 4.0.5 Source code file: gmx_sdf.c, line: 177 Fatal error: For single particle SDF, all reference groupsmust have the same size. --- Nilesh On Mon, May 17, 2010 8:23 pm, Dallas B. Warren wrote: Can you copy and paste into here what you see between: Select a reference group and 1 group And Select a group: When you run the script. Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When the only tool you own is a hammer, every problem begins to resemble a nail. -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users- boun...@gromacs.org] On Behalf Of Nilesh Dhumal Sent: Tuesday, 18 May 2010 9:29 AM To: Discussion list for GROMACS users Subject: RE: [gmx-users] g_sdf : error hey Sorry for typing mistake. I used ths command. g_sdf -f 3.trr -n glu-emi-cl-128-no.ndx -s 3.tpr -mode 1 -o sdf.plt -r Nilesh On Mon, May 17, 2010 6:37 pm, Dallas B. Warren wrote: g_sdf -f 3.trr -n glu-emi-cl-128-no.ndx -s -mode 1 3.tpr -o sdf.plt -r Is that the exact command line you used? If so, doubt it would actually work, since it should be: g_sdf -f 3.trr -n glu-emi-cl-128-no.ndx -s 3.tpr -mode 1 -o sdf.plt - r Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When the only tool you own is a hammer, every problem begins to resemble a nail. -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users- boun...@gromacs.org] On Behalf Of Nilesh Dhumal Sent: Tuesday, 18 May 2010 5:55 AM To: gmx-users@gromacs.org Subject: [gmx-users] g_sdf : error Hello, I am trying to run g_sdf for sovlation for glucose in ionic liquids. I am trying to find distribution of anion around glucose. g_sdf -f 3.trr -n glu-emi-cl-128-no.ndx -s -mode 1 3.tpr -o sdf.plt -r First three group I selected from the same residue (Glucose). Forth grouup I selected from as anion (Anion residue ). I am geting following error. Fatal error: For single particle SDF, all reference groupsmust have the same size. Thanks Nilesh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please
RE: [gmx-users] g_sdf : error
As I suspected: Group16 ( C2) has 129 elements Group17 ( C3) has 1 elements Group18 ( C4) has 129 elements As the error has told you, C3 does not have the same number of elements as C2 and C4. Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When the only tool you own is a hammer, every problem begins to resemble a nail. -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users- boun...@gromacs.org] On Behalf Of Nilesh Dhumal Sent: Tuesday, 18 May 2010 11:21 AM To: Discussion list for GROMACS users Subject: RE: [gmx-users] g_sdf : error Here are details. the first three groups from GUL residue and the last in cation (residue) Group 0 ( System) has 2584 elements Group 1 ( Protein) has 2456 elements Group 2 ( Protein-H) has 1036 elements Group 3 ( C-alpha) has 0 elements Group 4 (Backbone) has 128 elements Group 5 ( MainChain) has 129 elements Group 6 (MainChain+Cb) has 129 elements Group 7 ( MainChain+H) has 129 elements Group 8 ( SideChain) has 2327 elements Group 9 ( SideChain-H) has 907 elements Group10 ( Prot-Masses) has 2456 elements Group11 ( Non-Protein) has 128 elements Group12 ( CL) has 128 elements Group13 ( Other) has 128 elements Group14 ( GUL) has24 elements Group15 ( O) has 1 elements Group16 ( C2) has 129 elements Group17 ( C3) has 1 elements Group18 ( C4) has 129 elements Group19 ( C5) has 1 elements Group20 ( C6) has 129 elements -- -- Group39 ( EMI) has 2432 elements Group40 ( C) has 128 elements - - Group58 ( H19) has 128 elements Group59 ( CL) has 128 elements Group60 ( CL) has 128 elements Select a group: 16 Selected 16: 'C2' Select a group: 17 Selected 17: 'C3' Select a group: 18 Selected 18: 'C4' Select a group: 39 Selected 39: 'EMI' trn version: GMX_trn_file (single precision) Reading frame 0 time0.000 --- Program g_sdf, VERSION 4.0.5 Source code file: gmx_sdf.c, line: 177 Fatal error: For single particle SDF, all reference groupsmust have the same size. --- Nilesh On Mon, May 17, 2010 8:23 pm, Dallas B. Warren wrote: Can you copy and paste into here what you see between: Select a reference group and 1 group And Select a group: When you run the script. Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When the only tool you own is a hammer, every problem begins to resemble a nail. -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users- boun...@gromacs.org] On Behalf Of Nilesh Dhumal Sent: Tuesday, 18 May 2010 9:29 AM To: Discussion list for GROMACS users Subject: RE: [gmx-users] g_sdf : error hey Sorry for typing mistake. I used ths command. g_sdf -f 3.trr -n glu-emi-cl-128-no.ndx -s 3.tpr -mode 1 -o sdf.plt -r Nilesh On Mon, May 17, 2010 6:37 pm, Dallas B. Warren wrote: g_sdf -f 3.trr -n glu-emi-cl-128-no.ndx -s -mode 1 3.tpr -o sdf.plt -r Is that the exact command line you used? If so, doubt it would actually work, since it should be: g_sdf -f 3.trr -n glu-emi-cl-128-no.ndx -s 3.tpr -mode 1 -o sdf.plt - r Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When the only tool you own is a hammer, every problem begins to resemble a nail. -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users- boun...@gromacs.org] On Behalf Of Nilesh Dhumal Sent: Tuesday, 18 May 2010 5:55 AM To: gmx-users@gromacs.org Subject: [gmx-users] g_sdf : error Hello, I am trying to run g_sdf for sovlation for glucose in ionic liquids. I am trying to find distribution of anion around glucose. g_sdf -f 3.trr -n glu-emi-cl-128-no.ndx -s -mode 1 3.tpr -o sdf.plt -r First three group I selected from the same residue (Glucose). Forth grouup I selected from as anion (Anion residue ). I am geting
Re: [gmx-users] How to add an user-defined external potential
- Original Message - From: Sanku M msank...@yahoo.com Date: Tuesday, May 18, 2010 4:10 Subject: [gmx-users] How to add an user-defined external potential To: gmx-users@gromacs.org Hi, I am planning to add an external harmonic potential along z direction of a system : i.e U(z)= 0.5*K*z(**2) I was wondering if I can get an help on how to add an user-defined external potential like this in gromacs ? Thanks Sanku People may have constructive feedback, but you'll be largely on your own. My standard advice is to get out a debugger and step through the code on a small model system similar to your target system. In your case, you probably want to add code after/in do_force_lowlevel(). If you need the code to work in parallel, then you have some extra work interacting with the DD or PD algorithms, as each processor has only a subset of the atoms. If you want pressure coupling, you'll need to consider how your external potential should contribute to the virial. If you want PBC then you will get weird boundary effects. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: gmx-users Digest, Vol 73, Issue 98
Justin, Yes,it's fixed. Thank you. Zhang Cun Message: 1 Date: Mon, 17 May 2010 07:15:31 -0400 From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] About wiki error To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4bf12553.2070...@vt.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed Cun Zhang wrote: Hi, there seems two errors in the following page: http://www.gromacs.org/Documentation/Terminology/NVT say NVT is microcanonical ensemble. and http://www.gromacs.org/Documentation/Terminology/NVE say NVE is canonical ensemble. I register at wiki, but haven't authority to modify them. Can anybody fix them? Fixed. I think you need to contact Rossen to get editing permission on the site after you've registered. -Justin Thank you! Ref: http://en.wikipedia.org/wiki/Molecular_dynamics -- 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 -- Blog: http://www.edwardpku.com/cun -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] g_sdf : error
Thanks. Its working. Why all coordinates are zero in refmol.gro file. NIlesh On Mon, May 17, 2010 9:31 pm, Dallas B. Warren wrote: As I suspected: Group16 ( C2) has 129 elements Group17 ( C3) has 1 elements Group18 ( C4) has 129 elements As the error has told you, C3 does not have the same number of elements as C2 and C4. Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When the only tool you own is a hammer, every problem begins to resemble a nail. -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users- boun...@gromacs.org] On Behalf Of Nilesh Dhumal Sent: Tuesday, 18 May 2010 11:21 AM To: Discussion list for GROMACS users Subject: RE: [gmx-users] g_sdf : error Here are details. the first three groups from GUL residue and the last in cation (residue) Group 0 ( System) has 2584 elements Group 1 ( Protein) has 2456 elements Group 2 ( Protein-H) has 1036 elements Group 3 ( C-alpha) has 0 elements Group 4 (Backbone) has 128 elements Group 5 ( MainChain) has 129 elements Group 6 (MainChain+Cb) has 129 elements Group 7 ( MainChain+H) has 129 elements Group 8 ( SideChain) has 2327 elements Group 9 ( SideChain-H) has 907 elements Group10 ( Prot-Masses) has 2456 elements Group11 ( Non-Protein) has 128 elements Group12 ( CL) has 128 elements Group13 ( Other) has 128 elements Group14 ( GUL) has24 elements Group15 ( O) has 1 elements Group16 ( C2) has 129 elements Group17 ( C3) has 1 elements Group18 ( C4) has 129 elements Group19 ( C5) has 1 elements Group20 ( C6) has 129 elements -- -- Group39 ( EMI) has 2432 elements Group40 ( C) has 128 elements - - Group58 ( H19) has 128 elements Group59 ( CL) has 128 elements Group60 ( CL) has 128 elements Select a group: 16 Selected 16: 'C2' Select a group: 17 Selected 17: 'C3' Select a group: 18 Selected 18: 'C4' Select a group: 39 Selected 39: 'EMI' trn version: GMX_trn_file (single precision) Reading frame 0 time 0.000 --- Program g_sdf, VERSION 4.0.5 Source code file: gmx_sdf.c, line: 177 Fatal error: For single particle SDF, all reference groupsmust have the same size. --- Nilesh On Mon, May 17, 2010 8:23 pm, Dallas B. Warren wrote: Can you copy and paste into here what you see between: Select a reference group and 1 group And Select a group: When you run the script. Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When the only tool you own is a hammer, every problem begins to resemble a nail. -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users- boun...@gromacs.org] On Behalf Of Nilesh Dhumal Sent: Tuesday, 18 May 2010 9:29 AM To: Discussion list for GROMACS users Subject: RE: [gmx-users] g_sdf : error hey Sorry for typing mistake. I used ths command. g_sdf -f 3.trr -n glu-emi-cl-128-no.ndx -s 3.tpr -mode 1 -o sdf.plt -r Nilesh On Mon, May 17, 2010 6:37 pm, Dallas B. Warren wrote: g_sdf -f 3.trr -n glu-emi-cl-128-no.ndx -s -mode 1 3.tpr -o sdf.plt -r Is that the exact command line you used? If so, doubt it would actually work, since it should be: g_sdf -f 3.trr -n glu-emi-cl-128-no.ndx -s 3.tpr -mode 1 -o sdf.plt - r Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When the only tool you own is a hammer, every problem begins to resemble a nail. -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users- boun...@gromacs.org] On Behalf Of Nilesh Dhumal Sent: Tuesday, 18 May 2010 5:55 AM To: gmx-users@gromacs.org Subject: [gmx-users] g_sdf : error Hello, I am trying to run g_sdf for sovlation for glucose in ionic liquids. I am trying to find distribution of anion around glucose. g_sdf -f 3.trr -n glu-emi-cl-128-no.ndx -s -mode 1 3.tpr -o sdf.plt -r First three group I selected from the same residue (Glucose). Forth
[gmx-users] Computational Alanine Scanning
Dear all, I'm trying use GROMACS to calculate binding free energy with MM-PBSA method and do Computational Alanine Scanning. After run MD and obtain pdb files, I use PYMOL to mutate one residue to Alanine to estimate the energy difference between 2 structures. My issue is that I don't know how to generate topology file (.top file) after mutation but not ignore hydrogen in initial file. If using pdb2gmx command, it needs me ignore hydrogen and I think hydrogen after using this command is not in the same place with hydrogen at first. This will my my results unbelievable. Can any ones help me ?? With the best regards; Binh Khanh Mai -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Computational Alanine Scanning
- Original Message - From: Binh Khanh Mai khanhbinh...@yahoo.com Date: Tuesday, May 18, 2010 14:10 Subject: [gmx-users] Computational Alanine Scanning To: gmx-users@gromacs.org --- | Dear all, I'm trying use GROMACS to calculate binding free energy with MM-PBSA method and do Computational Alanine Scanning. After run MD and obtain pdb files, I use PYMOL to mutate one residue to Alanine to estimate the energy difference between 2 structures. My issue is that I don't know how to generate topology file (.top file) after mutation but not ignore hydrogen in initial file. If using pdb2gmx command, it needs me ignore hydrogen and I think hydrogen after using this command is not in the same place with hydrogen at first. This will my my results unbelievable. Do your mutation with PYMOL, and later plan to use those coordinates as inputs to grompp. Use pdb2gmx however you need to in order to create the new .top. Assuming PYMOL is not messing around with atom/residue naming and ordering except for the mutated residue, all you have to do is edit a copy of the PYMOL coordinate file so that the new residue has atom names, residue names and atom ordering that match the .top. Then supply the .top with the fixed coordinate file to grompp. Alternatively, work out why pdb2gmx requires you to ignore and regenerate hydrogens, and fix the issue there. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
