RE: [gmx-users] Setting up an infinitely hard wall
Hi, I have obtained distributions with in infinite wall by simulating with an softer wall and unbiasing with configurations with the wall potential. But if you need the dynamics, or you want less hassle during the simulation, you will have to do a bit more effort in coding an infinitely hard wall. You will not only have to inverse the velocity, but also mirror the position of the particle in the wall. This should on require a few lines of code in do_update_md in src/mdlib/update.c. Note that this will only work easily when you do not have constraints present. With constraints things get much more complicated. Berk Date: Thu, 22 Oct 2009 14:34:06 -0700 From: kgp.a...@gmail.com To: gmx-users@gromacs.org Subject: [gmx-users] Setting up an infinitely hard wall Hi everyone, I am sending this email again hoping for any quick input for my question. I have been trying to set up an infinitely hard potential wall. I tried to use the available wall options and could not really get it to do what i needed. I wanted a steep repulsive potential but when i created that, the system was blowing up, reason being that it requires smaller time step and i cant afford to have smaller time step. My idea to overcome this issue is to just reverse the velocity of the particle whenever it hits the wall. I am not sure if there is any thing in GROMACS which does this but any suggestions will be very helpful. If there is nothing set up for something like above, i would like to play around with the code to figure it out. If this is the case, could somebody direct me to a starting point. Thank you Amit _ New Windows 7: Find the right PC for you. Learn more. http://windows.microsoft.com/shop___ 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] Setting up an infinitely hard wall
Hi Berk, Thank you for the response. I have obtained distributions with in infinite wall by simulating with an softer wall and unbiasing with configurations with the wall potential. Could you explain the above ? I am not sure if i get your point. But if you need the dynamics, or you want less hassle during the simulation, you will have to do a bit more effort in coding an infinitely hard wall. You will not only have to inverse the velocity, but also mirror the position of the particle in the wall. That's true. I am sorry i didnt mention that. This should on require a few lines of code in do_update_md in src/mdlib/update.c. Great, I will try this as soon as possible. Note that this will only work easily when you do not have constraints present. With constraints things get much more complicated. I do have constraints present. Thank you for pointing this. I am working with SPC water and I should, in principle be able to figure out the co-ordinates of all atoms in the molecule if I am given one of the water's atom's co-ordinate. Does that sound ok? Thanks for the input again, Amit Berk -- Date: Thu, 22 Oct 2009 14:34:06 -0700 From: kgp.a...@gmail.com To: gmx-users@gromacs.org Subject: [gmx-users] Setting up an infinitely hard wall Hi everyone, I am sending this email again hoping for any quick input for my question. I have been trying to set up an infinitely hard potential wall. I tried to use the available wall options and could not really get it to do what i needed. I wanted a steep repulsive potential but when i created that, the system was blowing up, reason being that it requires smaller time step and i cant afford to have smaller time step. My idea to overcome this issue is to just reverse the velocity of the particle whenever it hits the wall. I am not sure if there is any thing in GROMACS which does this but any suggestions will be very helpful. If there is nothing set up for something like above, i would like to play around with the code to figure it out. If this is the case, could somebody direct me to a starting point. Thank you Amit -- New Windows 7: Find the right PC for you. Learn more.http://windows.microsoft.com/shop ___ 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] POPG-Martini Force Field
On Oct 22, 2009, at 11:28 PM, Amit Choubey wrote: On Thu, Oct 22, 2009 at 9:53 AM, S hv sola...@hotmail.com wrote: Hi, I am currently working with peptide/lipids interactions using the martini force field. I want to built a bacterial membrane, so I trying to find the topology of the POPG lipid but until now without success. In the martini_v2.0_lipids.itp file, the PG lipids are no included. I have seen some works using the martini force field and POPG lipids, e.g., The molecular mechanism monolayer PNAS 105, 10803-10808, but they don't specify the topology of POPG lipids. You can do this on your own just pull out the atomic structure of DPPC and POPG from any website. Compare atomistic DPPC with the Coarse Grained DPPC and it wont be hard to figure out the POPG CG topology. That is certainly not that easy. A lot of parameterizations efforts have to be involved. BTW, the paper does give a short description about the topology of POPG The best is probably to ask the authors of that paper to share their topology, which they should. I also tried in the martini web page, but I just found the martini_v2.0_lipids.itp file. Could anyone help me to find such topology? Thanks a lot for your time, Salvador Windows Live: Make it easier for your friends to see what you’re up to on Facebook. ___ 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] POPG-Martini Force Field
On Fri, Oct 23, 2009 at 12:33 AM, XAvier Periole x.peri...@rug.nl wrote: On Oct 22, 2009, at 11:28 PM, Amit Choubey wrote: On Thu, Oct 22, 2009 at 9:53 AM, S hv sola...@hotmail.com wrote: Hi, I am currently working with peptide/lipids interactions using the martini force field. I want to built a bacterial membrane, so I trying to find the topology of the POPG lipid but until now without success. In the martini_v2.0_lipids.itp file, the PG lipids are no included. I have seen some works using the martini force field and POPG lipids, e.g., The molecular mechanism monolayer PNAS 105, 10803-10808, but they don't specify the topology of POPG lipids. You can do this on your own just pull out the atomic structure of DPPC and POPG from any website. Compare atomistic DPPC with the Coarse Grained DPPC and it wont be hard to figure out the POPG CG topology. That is certainly not that easy. A lot of parameterizations efforts have to be involved. No, thats easy because you are working with a coarse grained model. There are are only few types of particles possible. The only tricky ones are the head groups which the paper does mention. BTW, the paper does give a short description about the topology of POPG The best is probably to ask the authors of that paper to share their topology, which they should. I also tried in the martini web page, but I just found the martini_v2.0_lipids.itp file. Could anyone help me to find such topology? Thanks a lot for your time, Salvador -- Windows Live: Make it easier for your friends to see what you’re up to on Facebook.http://www.microsoft.com/middleeast/windows/windowslive/see-it-in-action/social-network-basics.aspx?ocid=PID23461::T:WLMTAGL:ON:WL:en-xm:SI_SB_2:092009 ___ 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] Setting up an infinitely hard wall
Hi, If you have a wall potential, you can reweight the configurations with weight 0 if one or more particles are beyond the wall and exp(Vwall/kT) if no particles are beyond the wall. This will only work efficiently if you choose the wall potential in a smart way. I managed to get an efficiency of 70%. If you have constraints, an atom that goes beyond the wall is directly coupled to the atoms it is constrained to. You will have to work out the equations for such a situation. It might be as simple that you can just correct x and v for the atom that went beyond the wall and then apply the constraints as normal. Berk Date: Fri, 23 Oct 2009 00:26:08 -0700 Subject: Re: [gmx-users] Setting up an infinitely hard wall From: kgp.a...@gmail.com To: gmx-users@gromacs.org Hi Berk, Thank you for the response. I have obtained distributions with in infinite wall by simulating with an softer wall and unbiasing with configurations with the wall potential. Could you explain the above ? I am not sure if i get your point. But if you need the dynamics, or you want less hassle during the simulation, you will have to do a bit more effort in coding an infinitely hard wall. You will not only have to inverse the velocity, but also mirror the position of the particle in the wall. That's true. I am sorry i didnt mention that. This should on require a few lines of code in do_update_md in src/mdlib/update.c. Great, I will try this as soon as possible. Note that this will only work easily when you do not have constraints present. With constraints things get much more complicated. I do have constraints present. Thank you for pointing this. I am working with SPC water and I should, in principle be able to figure out the co-ordinates of all atoms in the molecule if I am given one of the water's atom's co-ordinate. Does that sound ok? Thanks for the input again,Amit Berk Date: Thu, 22 Oct 2009 14:34:06 -0700 From: kgp.a...@gmail.com To: gmx-users@gromacs.org Subject: [gmx-users] Setting up an infinitely hard wall Hi everyone, I am sending this email again hoping for any quick input for my question. I have been trying to set up an infinitely hard potential wall. I tried to use the available wall options and could not really get it to do what i needed. I wanted a steep repulsive potential but when i created that, the system was blowing up, reason being that it requires smaller time step and i cant afford to have smaller time step. My idea to overcome this issue is to just reverse the velocity of the particle whenever it hits the wall. I am not sure if there is any thing in GROMACS which does this but any suggestions will be very helpful. If there is nothing set up for something like above, i would like to play around with the code to figure it out. If this is the case, could somebody direct me to a starting point. Thank you Amit New Windows 7: Find the right PC for you. Learn more. ___ 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 _ Express yourself instantly with MSN Messenger! Download today it's FREE! http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/___ gmx-users mailing listgmx-users@gromacs.org http://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] POPG-Martini Force Field
On Oct 23, 2009, at 9:45 AM, Amit Choubey wrote: On Fri, Oct 23, 2009 at 12:33 AM, XAvier Periole x.peri...@rug.nl wrote: On Oct 22, 2009, at 11:28 PM, Amit Choubey wrote: On Thu, Oct 22, 2009 at 9:53 AM, S hv sola...@hotmail.com wrote: Hi, I am currently working with peptide/lipids interactions using the martini force field. I want to built a bacterial membrane, so I trying to find the topology of the POPG lipid but until now without success. In the martini_v2.0_lipids.itp file, the PG lipids are no included. I have seen some works using the martini force field and POPG lipids, e.g., The molecular mechanism monolayer PNAS 105, 10803-10808, but they don't specify the topology of POPG lipids. You can do this on your own just pull out the atomic structure of DPPC and POPG from any website. Compare atomistic DPPC with the Coarse Grained DPPC and it wont be hard to figure out the POPG CG topology. That is certainly not that easy. A lot of parameterizations efforts have to be involved. No, thats easy because you are working with a coarse grained model. There are are only few types of particles possible. The only tricky ones are the head groups which the paper does mention. If the bead type is given in the paper then the work is easier. My point is that assimilate CG with simple is a big mistake! BTW, the paper does give a short description about the topology of POPG The best is probably to ask the authors of that paper to share their topology, which they should. I also tried in the martini web page, but I just found the martini_v2.0_lipids.itp file. Could anyone help me to find such topology? Thanks a lot for your time, Salvador Windows Live: Make it easier for your friends to see what you’re up to on Facebook. ___ 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 ___ 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: Chloroform (CHCl3) solvent box for G53a5 force field
Following up on the previous message, I noticed that the topology I previously sent (including 10 bonds) works for a minimization, but not for an MD simulation. grompp issues the following warning: WARNING 1 [file topol.top, line 29]: Molecule type 'CHCL3' has 10 constraints. For stability and efficiency there should not be more constraints than internal number of degrees of freedom: 9. I therefore used the following .itp file, with only the C-H and C-Cl bonds: --[chcl3.itp]-- [ moleculetype ] ; Namenrexcl CHCL3 1 [ atoms ] ; nr type resnr residue atom cgnr charge mass typeBchargeB massB 1 HCHL 1 CHCL3 HChL 1 0.082 1.008 2 CCHL 1 CHCL3 CChL 1 0.179 12.011 3 CLCHL 1 CHCL3 CLCh1 1 -0.087 35.453 4 CLCHL 1 CHCL3 CLCh2 1 -0.087 35.453 5 CLCHL 1 CHCL3 CLCh3 1 -0.087 35.453 [ bonds ] ; aiaj functc0c1c2c3 1 2 2gb_39 2 3 2gb_40 2 4 2gb_40 2 5 2gb_40 [ angles ] ; aiajak functc0c1 c2c3 1 2 3 2 ga_43 1 2 4 2 ga_43 1 2 5 2 ga_43 3 2 4 2 ga_44 3 2 5 2 ga_44 4 2 5 2 ga_44 [ exclusions ] 1 2 3 4 5 2 1 3 4 5 3 1 2 4 5 4 1 2 3 5 5 1 2 3 4 --[chcl3.itp]-- These are the steps I took: - build a box with 216 CHCL3 molecules with genbox - adjusted the density to 1479 with editconf - minimized the box to F100 (steep, 5 steps) - equilibrated NVT (position restrained C), 100ps, 300K, tau_t 0.1 - equilibrated NPT (position restrained C), 100ps, 300K, 1bar, tau_t 0.1, tau_p 2.0, compressibility 1e-4 (from CRC handbook) Until here, everything looks decent, except for relatively large fluctuations in T (RMSD ~9K) and density (RMSD ~10kg m-3). I then performed an unconstrained MD, 1ns, otherwise identical parameters to NPT equilibration. Temp (300K) and density (1450 kg m-3) stable, but fluctuating (RMSD 8 and 20 respectively). In order to compare the results with Tironi and van Gunsteren, Molecular Physics 1994, 83, 381, who used the same GROMOS parameters: Epot = -28.6 +/- 0.3 kJ/mol, density 1520 +/- 12 kg m-3. This is the output I get from g_energy: Energy Average RMSD Fluct. Drift Tot-Drift --- Potential -4720.16119.141118.978 -0.0215895 -21.5896 Therefore molar Epot = -(-4720)/216 = 21.9 kJ/mol. What factors could be accountable for the decrease wrt the reported value of 28.4? Experimental deltaHv is 31.4 kJ/mol (same reference). Would there be any other parameters I should check before using this solvent box in production runs? Regards, Pablo -- Pablo Englebienne, PhD Institute of Complex Molecular Systems (ICMS) Eindhoven University of Technology, TU/e PO Box 513, HG -1.26 5600 MB Eindhoven, The Netherlands Tel +31 40 247 5349 ___ 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 stop duplicate atoms from being deleted
Hello I am studying a mesoporous silica for which there is no topology in gromacs-to try to automate the process of generating a topology file (x2top doesn?t work), I am using pdb2gmx (or rather trying to). I have parameters for my silica structure and have added a new section for my molecule to the .rtp file, .atp file, atommass.dat, atom_nom.dbl, nb.itp and bon.itp files. The problem is that when I use my .pdb file to generate a topology, pdb2gmx checks for duplicates and removes almost all of my atoms. It leaves only one of each type. I should have a few hundred of each atom type?here is the output from pdb2gmx? Analyzing pdb file There are 1 chains and 0 blocks of water and 1 residues with 4284 atoms chain #res #atoms 1 ' ' 1 4284 All occupancies are one All ok up to here?and then?. Processing chain 1 (4284 atoms, 1 residues) There are 552 donors and 2580 acceptors There are 1603 hydrogen bonds Checking for duplicate atoms Now there are 4 atoms. Deleted 4280 duplicates. Can anyone explain why this is happening? ?none of my atoms have the same coordinates. Is there a file that I have forgotten to alter? Is there is fix to turn off the checking of duplicate atoms? I don?t want any of my atoms to be deleted! Below I paste an extract of my pdb file? CRYST1 46.421 43.630 75.838 90.00 90.00 120.00 P 1 1 ATOM 1 SI MCM 1 -21.090 -1.951 -29.596 1.00 0.00 SI ATOM 2 SI MCM 1 -21.090 -1.951 -10.636 1.00 0.00 SI ??.. ATOM 1153 OMCM 1 20.602 -18.404 -20.904 1.00 0.00 O ATOM 1154 OMCM 1 20.602 -18.404 -1.945 1.00 0.00 O ? ATOM 3181 OH MCM 1 -6.620 -18.769 -32.169 1.00 0.00 ATOM 3182 OH MCM 1 -6.620 -18.769 -13.210 1.00 0.00 . ATOM 3733 HMCM 1 -6.674 -18.381 -33.035 1.00 0.00 H ATOM 3734 HMCM 1 -6.616 -18.600 -14.144 1.00 0.00 H Any advice appreciated, Thanks in advance -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. ___ 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] how to stop duplicate atoms from being deleted
Quoting Jennifer Williams jennifer.willi...@ed.ac.uk: Hello I am studying a mesoporous silica for which there is no topology in gromacs-to try to automate the process of generating a topology file (x2top doesn?t work), I am using pdb2gmx (or rather trying to). I have parameters for my silica structure and have added a new section for my molecule to the .rtp file, .atp file, atommass.dat, atom_nom.dbl, nb.itp and bon.itp files. The problem is that when I use my .pdb file to generate a topology, pdb2gmx checks for duplicates and removes almost all of my atoms. It leaves only one of each type. I should have a few hundred of each atom type?here is the output from pdb2gmx? Analyzing pdb file There are 1 chains and 0 blocks of water and 1 residues with 4284 atoms chain #res #atoms 1 ' ' 1 4284 All occupancies are one All ok up to here?and then?. Processing chain 1 (4284 atoms, 1 residues) There are 552 donors and 2580 acceptors There are 1603 hydrogen bonds Checking for duplicate atoms Now there are 4 atoms. Deleted 4280 duplicates. Can anyone explain why this is happening? ?none of my atoms have the same coordinates. Is there a file that I have forgotten to alter? Is there is fix to turn off the checking of duplicate atoms? I don?t want any of my atoms to be deleted! You have all of your atoms defined within one residue. I'm assuming your .rtp entry contains the definition of a single repeat unit, so each monomer should be a separate residue. The coordinates don't matter, it's because within each residue, you have the same atom names, so pdb2gmx removes them when it finds them. Below I paste an extract of my pdb file? I'm assuming you'll have to probably reconstruct this file to re-organize the atoms to define continuous residues. It appears they are grouped by atom name, which is probably not what you want. -Justin CRYST1 46.421 43.630 75.838 90.00 90.00 120.00 P 1 1 ATOM 1 SI MCM 1 -21.090 -1.951 -29.596 1.00 0.00 SI ATOM 2 SI MCM 1 -21.090 -1.951 -10.636 1.00 0.00 SI ??.. ATOM 1153 OMCM 1 20.602 -18.404 -20.904 1.00 0.00 O ATOM 1154 OMCM 1 20.602 -18.404 -1.945 1.00 0.00 O ? ATOM 3181 OH MCM 1 -6.620 -18.769 -32.169 1.00 0.00 ATOM 3182 OH MCM 1 -6.620 -18.769 -13.210 1.00 0.00 . ATOM 3733 HMCM 1 -6.674 -18.381 -33.035 1.00 0.00 H ATOM 3734 HMCM 1 -6.616 -18.600 -14.144 1.00 0.00 H Any advice appreciated, Thanks in advance -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA jalem...@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] Re: Chloroform (CHCl3) solvent box for G53a5 force field
Pablo Englebienne wrote: Following up on the previous message, I noticed that the topology I previously sent (including 10 bonds) works for a minimization, but not for an MD simulation. grompp issues the following warning: WARNING 1 [file topol.top, line 29]: Molecule type 'CHCL3' has 10 constraints. For stability and efficiency there should not be more constraints than internal number of degrees of freedom: 9. I therefore used the following .itp file, with only the C-H and C-Cl bonds: If bonds are supposed to be defined between, i.e. H-Cl and Cl-Cl, then this may not be appropriate. Instead, you could perhaps set the covalent bonds as [constraints] in the topology, leaving the other nonbonded bonds as [bonds] (and then use constraints = none in the .mdp file, so only the [constraints] are used). --[chcl3.itp]-- [ moleculetype ] ; Namenrexcl CHCL3 1 [ atoms ] ; nr type resnr residue atom cgnr charge mass typeBchargeB massB 1 HCHL 1 CHCL3 HChL 1 0.082 1.008 2 CCHL 1 CHCL3 CChL 1 0.179 12.011 3 CLCHL 1 CHCL3 CLCh1 1 -0.087 35.453 4 CLCHL 1 CHCL3 CLCh2 1 -0.087 35.453 5 CLCHL 1 CHCL3 CLCh3 1 -0.087 35.453 [ bonds ] ; aiaj functc0c1c2c3 1 2 2gb_39 2 3 2gb_40 2 4 2gb_40 2 5 2gb_40 [ angles ] ; aiajak functc0c1 c2c3 1 2 3 2 ga_43 1 2 4 2 ga_43 1 2 5 2 ga_43 3 2 4 2 ga_44 3 2 5 2 ga_44 4 2 5 2 ga_44 [ exclusions ] 1 2 3 4 5 2 1 3 4 5 3 1 2 4 5 4 1 2 3 5 5 1 2 3 4 --[chcl3.itp]-- These are the steps I took: - build a box with 216 CHCL3 molecules with genbox - adjusted the density to 1479 with editconf - minimized the box to F100 (steep, 5 steps) - equilibrated NVT (position restrained C), 100ps, 300K, tau_t 0.1 - equilibrated NPT (position restrained C), 100ps, 300K, 1bar, tau_t 0.1, tau_p 2.0, compressibility 1e-4 (from CRC handbook) What is the purpose of position restraints here? Until here, everything looks decent, except for relatively large fluctuations in T (RMSD ~9K) and density (RMSD ~10kg m-3). Probably a consequence of restraining the starting structure. I'd say you're not equilibrating appropriately with position restraints imposed. I then performed an unconstrained MD, 1ns, otherwise identical parameters to NPT equilibration. Temp (300K) and density (1450 kg m-3) stable, but fluctuating (RMSD 8 and 20 respectively). In order to compare the results with Tironi and van Gunsteren, Molecular Physics 1994, 83, 381, who used the same GROMOS parameters: Epot = -28.6 +/- 0.3 kJ/mol, density 1520 +/- 12 kg m-3. This is the output I get from g_energy: Energy Average RMSD Fluct. Drift Tot-Drift --- Potential -4720.16119.141118.978 -0.0215895 -21.5896 Therefore molar Epot = -(-4720)/216 = 21.9 kJ/mol. What factors could be accountable for the decrease wrt the reported value of 28.4? Experimental deltaHv is 31.4 kJ/mol (same reference). Insufficient equilibration, and a variety of factors within the .mdp file. If you want feedback on run parameters, you'll have to post the .mdp. -Justin Would there be any other parameters I should check before using this solvent box in production runs? Regards, Pablo -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] how to stop duplicate atoms from being deleted
Hi Justin, Thanks for the reply. I am in fact studying one huge molecule. All of my atoms are bonded together in one large structure (kind of like a zeolite) so I have necessarily defined them as a single residue. There is no way I can split this molecule into smaller subunits and thus define a number of residues-it wouldn't make sense to do so. Yes in my .rtp file I have only defined each atom type once. To define each and every atom in my one residue would mean defining 4284 atoms! I am having real trouble in creating topology files for my structure. At the moment, the only way I can do this is by using a tool in DL_POLY to create a field file and then manually change it to a .top file. This is really fiddely and I have a number of similar structures to do this for. I was hoping that I could do a similar step in Gromacs and get a .top file straight away-even if it means a bit more work setting it up. Is there any hope or is pdb2gmx simply not designed to work for this sort of system? Thanks Jenny Quoting Justin A. Lemkul jalem...@vt.edu: Quoting Jennifer Williams jennifer.willi...@ed.ac.uk: Hello I am studying a mesoporous silica for which there is no topology in gromacs-to try to automate the process of generating a topology file (x2top doesn?t work), I am using pdb2gmx (or rather trying to). I have parameters for my silica structure and have added a new section for my molecule to the .rtp file, .atp file, atommass.dat, atom_nom.dbl, nb.itp and bon.itp files. The problem is that when I use my .pdb file to generate a topology, pdb2gmx checks for duplicates and removes almost all of my atoms. It leaves only one of each type. I should have a few hundred of each atom type?here is the output from pdb2gmx? Analyzing pdb file There are 1 chains and 0 blocks of water and 1 residues with 4284 atoms chain #res #atoms 1 ' ' 1 4284 All occupancies are one All ok up to here?and then?. Processing chain 1 (4284 atoms, 1 residues) There are 552 donors and 2580 acceptors There are 1603 hydrogen bonds Checking for duplicate atoms Now there are 4 atoms. Deleted 4280 duplicates. Can anyone explain why this is happening? ?none of my atoms have the same coordinates. Is there a file that I have forgotten to alter? Is there is fix to turn off the checking of duplicate atoms? I don?t want any of my atoms to be deleted! You have all of your atoms defined within one residue. I'm assuming your .rtp entry contains the definition of a single repeat unit, so each monomer should be a separate residue. The coordinates don't matter, it's because within each residue, you have the same atom names, so pdb2gmx removes them when it finds them. Below I paste an extract of my pdb file? I'm assuming you'll have to probably reconstruct this file to re-organize the atoms to define continuous residues. It appears they are grouped by atom name, which is probably not what you want. -Justin CRYST1 46.421 43.630 75.838 90.00 90.00 120.00 P 1 1 ATOM 1 SI MCM 1 -21.090 -1.951 -29.596 1.00 0.00 SI ATOM 2 SI MCM 1 -21.090 -1.951 -10.636 1.00 0.00 SI ??.. ATOM 1153 OMCM 1 20.602 -18.404 -20.904 1.00 0.00 O ATOM 1154 OMCM 1 20.602 -18.404 -1.945 1.00 0.00 O ? ATOM 3181 OH MCM 1 -6.620 -18.769 -32.169 1.00 0.00 ATOM 3182 OH MCM 1 -6.620 -18.769 -13.210 1.00 0.00 . ATOM 3733 HMCM 1 -6.674 -18.381 -33.035 1.00 0.00 H ATOM 3734 HMCM 1 -6.616 -18.600 -14.144 1.00 0.00 H Any advice appreciated, Thanks in advance -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA jalem...@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 Dr. Jennifer Williams Institute for
Re: [gmx-users] how to stop duplicate atoms from being deleted
Jennifer Williams wrote: Hi Justin, Thanks for the reply. I am in fact studying one huge molecule. All of my atoms are bonded together in one large structure (kind of like a zeolite) so I have necessarily defined them as a single residue. I would argue that you have a polymer, which can certainly be handled by pdb2gmx. See below. There is no way I can split this molecule into smaller subunits and thus define a number of residues-it wouldn't make sense to do so. If you have a lot of repetition, I would think it would be quite easy to split it apart. Yes in my .rtp file I have only defined each atom type once. To define each and every atom in my one residue would mean defining 4284 atoms! If you have a repeating structure, you have a polymer, so you can just decompose a repeat unit into a single .rtp entry. That's the entire purpose of pdb2gmx, we certainly wouldn't want to create an .rtp entry for every single possible protein either! For more information, see here: http://www.gromacs.org/Documentation/How-tos/Polymers I am having real trouble in creating topology files for my structure. At the moment, the only way I can do this is by using a tool in DL_POLY to create a field file and then manually change it to a .top file. This is really fiddely and I have a number of similar structures to do this for. I was hoping that I could do a similar step in Gromacs and get a .top file straight away-even if it means a bit more work setting it up. Is there any hope or is pdb2gmx simply not designed to work for this sort of system? You can certainly use pdb2gmx, it is intended to be versatile so it can be used with any repeating structure of monomers, homogenous (like a repeating polymer) or heterogenous (like a protein). See the link above. -Justin Thanks Jenny Quoting Justin A. Lemkul jalem...@vt.edu: Quoting Jennifer Williams jennifer.willi...@ed.ac.uk: Hello I am studying a mesoporous silica for which there is no topology in gromacs-to try to automate the process of generating a topology file (x2top doesn?t work), I am using pdb2gmx (or rather trying to). I have parameters for my silica structure and have added a new section for my molecule to the .rtp file, .atp file, atommass.dat, atom_nom.dbl, nb.itp and bon.itp files. The problem is that when I use my .pdb file to generate a topology, pdb2gmx checks for duplicates and removes almost all of my atoms. It leaves only one of each type. I should have a few hundred of each atom type?here is the output from pdb2gmx? Analyzing pdb file There are 1 chains and 0 blocks of water and 1 residues with 4284 atoms chain #res #atoms 1 ' ' 1 4284 All occupancies are one All ok up to here?and then?. Processing chain 1 (4284 atoms, 1 residues) There are 552 donors and 2580 acceptors There are 1603 hydrogen bonds Checking for duplicate atoms Now there are 4 atoms. Deleted 4280 duplicates. Can anyone explain why this is happening? ?none of my atoms have the same coordinates. Is there a file that I have forgotten to alter? Is there is fix to turn off the checking of duplicate atoms? I don?t want any of my atoms to be deleted! You have all of your atoms defined within one residue. I'm assuming your .rtp entry contains the definition of a single repeat unit, so each monomer should be a separate residue. The coordinates don't matter, it's because within each residue, you have the same atom names, so pdb2gmx removes them when it finds them. Below I paste an extract of my pdb file? I'm assuming you'll have to probably reconstruct this file to re-organize the atoms to define continuous residues. It appears they are grouped by atom name, which is probably not what you want. -Justin CRYST1 46.421 43.630 75.838 90.00 90.00 120.00 P 1 1 ATOM 1 SI MCM 1 -21.090 -1.951 -29.596 1.00 0.00 SI ATOM 2 SI MCM 1 -21.090 -1.951 -10.636 1.00 0.00 SI ??.. ATOM 1153 OMCM 1 20.602 -18.404 -20.904 1.00 0.00 O ATOM 1154 OMCM 1 20.602 -18.404 -1.945 1.00 0.00 O ? ATOM 3181 OH MCM 1 -6.620 -18.769 -32.169 1.00 0.00 ATOM 3182 OH MCM 1 -6.620 -18.769 -13.210 1.00 0.00 . ATOM 3733 HMCM 1 -6.674 -18.381 -33.035 1.00 0.00 H ATOM 3734 HMCM 1 -6.616 -18.600 -14.144 1.00 0.00 H Any advice appreciated, Thanks in advance -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. ___ 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?
Re: [gmx-users] scripts to generate topology CG
Hello Sunny: I had already generated a valid .itp file for my protein using seq2itp. That .itp works for both the protein itself and the protein graphically inserted into a bilayer. When I add graphically further water it does not work any more. I thought there is something else that manages water without putting it everywhere. That script does not help. thanks francesco On Wed, Oct 21, 2009 at 3:46 PM, sunny mishra mishra.su...@gmail.com wrote: There is a seq2itp.pl script provided by martini folks in their website. You can get it from there. Sunny On Wed, Oct 21, 2009 at 9:42 AM, Francesco Pietra francesco.pie...@accademialucchese.it wrote: Hi: I am looking for scripts that generate topology in coarse grained. Thanks for indications. francesco pietra ___ 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-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 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] scripts to generate topology CG
Francesco Pietra wrote: Hello Sunny: I had already generated a valid .itp file for my protein using seq2itp. That .itp works for both the protein itself and the protein graphically inserted into a bilayer. When I add graphically further water it does not work any more. I thought there is something else that manages water without putting it everywhere. That script does not help. In order to get a solution to your problem, I think you're going to have to explain your methodology more clearly, including command lines and actual error messages. How are you adding water graphically? Is genbox not working? Can you not simply grep for the number of water molecules, i.e.: grep W solvated.gro | wc -l and use that number in the topology? -Justin thanks francesco On Wed, Oct 21, 2009 at 3:46 PM, sunny mishra mishra.su...@gmail.com wrote: There is a seq2itp.pl script provided by martini folks in their website. You can get it from there. Sunny On Wed, Oct 21, 2009 at 9:42 AM, Francesco Pietra francesco.pie...@accademialucchese.it wrote: Hi: I am looking for scripts that generate topology in coarse grained. Thanks for indications. francesco pietra ___ 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 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] how to calculate the vaporation enthalpy of pure small organic compound
Hi gmx-users, I want to calcualted the the vaporation enthalpy of benzaldehyde I think that the the vaporation enthalpy is the sum of non-bond interacion among the benzaldehyde molecule. So I made a NPT system simulation including 512 benzaldehyde molecule. The following is the intermolecule nonbond interaction using the g_energy. LJ-(SR)= -21128.7 Kj/mol LJ-(LR)= -889.855 Kj/mol Coulomb-(SR)= -3884.6 Kj/mol Coul.-recip = -2261.51 Kj/mol the sum of non-bond interaction = LJ-(SR) + LJ-(LR) + Coulomb-(SR) + Coul.-recip = 28164.665 Kj/mol But the experimental value of he vaporation enthalpy = 50.3 Kj/mol I have no ideal that why they have so much different. Now I don't know how to solve it. Any suggestion will be appreciated. This following is my md.mdp file. title = fws cpp = /usr/bin/cpp constraints = all-bonds integrator = md dt = 0.002; ps ! nsteps = 50 ; total 1ns nstcomm = 1 nstxout = 500 nstvout = 0 nstfout = 0 nstlist = 10 ns_type = grid rlist = 1.0 coulombtype = PME rcoulomb= 1.0 vdwtype = cut-off rvdw= 1.4 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 6 ewald_rtol = 1e-5 optimize_fft= yes ; Berendsen temperature coupling is on in three groups Tcoupl = berendsen tau_t = 0.1 tc_grps = system ref_t = 298.15 ; Pressure coupling is on Pcoupl = berendsen tau_p = 2.0 compressibility = 4.6e-5 ref_p = 1.0 ; Generate velocites is on at 323.15 K. gen_vel = yes gen_temp= 298.15 gen_seed = 173529 Jinyao Wang wan...@ciac.jl.cn 2009-10-23 ___ 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] how to calculate the vaporation enthalpy of pure small organic compound
Jinyao Wang wrote: Hi gmx-users, I want to calcualted the the vaporation enthalpy of benzaldehyde I think that the the vaporation enthalpy is the sum of non-bond interacion among the benzaldehyde molecule. So I made a NPT system simulation including 512 benzaldehyde molecule. The following is the intermolecule nonbond interaction using the g_energy. LJ-(SR)= -21128.7 Kj/mol LJ-(LR)= -889.855 Kj/mol Coulomb-(SR)= -3884.6 Kj/mol Coul.-recip = -2261.51 Kj/mol the sum of non-bond interaction = LJ-(SR) + LJ-(LR) + Coulomb-(SR) + Coul.-recip = 28164.665 Kj/mol But the experimental value of he vaporation enthalpy = 50.3 Kj/mol I have no ideal that why they have so much different. Now I don't know how to solve it. Any suggestion will be appreciated. These are totals for the intermolecular energy of the system. I'm guessing you didn't use -nmol 512 to calculate these results? -Justin This following is my md.mdp file. title = fws cpp = /usr/bin/cpp constraints = all-bonds integrator = md dt = 0.002; ps ! nsteps = 50 ; total 1ns nstcomm = 1 nstxout = 500 nstvout = 0 nstfout = 0 nstlist = 10 ns_type = grid rlist = 1.0 coulombtype = PME rcoulomb= 1.0 vdwtype = cut-off rvdw= 1.4 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 6 ewald_rtol = 1e-5 optimize_fft= yes ; Berendsen temperature coupling is on in three groups Tcoupl = berendsen tau_t = 0.1 tc_grps = system ref_t = 298.15 ; Pressure coupling is on Pcoupl = berendsen tau_p = 2.0 compressibility = 4.6e-5 ref_p = 1.0 ; Generate velocites is on at 323.15 K. gen_vel = yes gen_temp= 298.15 gen_seed = 173529 Jinyao Wang wan...@ciac.jl.cn 2009-10-23 ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] how to calculate the vaporation enthalpy of pure small organic compound
Justin A. Lemkul wrote: Jinyao Wang wrote: Hi gmx-users, I want to calcualted the the vaporation enthalpy of benzaldehyde I think that the the vaporation enthalpy is the sum of non-bond interacion among the benzaldehyde molecule.So I made a NPT system simulation including 512 benzaldehyde molecule. The following is the intermolecule nonbond interaction using the g_energy. LJ-(SR)= -21128.7 Kj/mol LJ-(LR)= -889.855 Kj/mol Coulomb-(SR)= -3884.6 Kj/mol Coul.-recip = -2261.51 Kj/mol the sum of non-bond interaction = LJ-(SR) + LJ-(LR) + Coulomb-(SR) + Coul.-recip = 28164.665 Kj/mol But the experimental value of he vaporation enthalpy = 50.3 Kj/mol I have no ideal that why they have so much different. Now I don't know how to solve it. Any suggestion will be appreciated. These are totals for the intermolecular energy of the system. I'm guessing you didn't use -nmol 512 to calculate these results? And then subtract the gas-phase energy (with com removed) and add kT. -Justin This following is my md.mdp file. title = fws cpp = /usr/bin/cpp constraints = all-bonds integrator = md dt = 0.002; ps ! nsteps = 50 ; total 1ns nstcomm = 1 nstxout = 500 nstvout = 0 nstfout = 0 nstlist = 10 ns_type = grid rlist = 1.0 coulombtype = PME rcoulomb= 1.0 vdwtype = cut-off rvdw= 1.4 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 6 ewald_rtol = 1e-5 optimize_fft= yes ; Berendsen temperature coupling is on in three groups Tcoupl = berendsen tau_t = 0.1 tc_grps = system ref_t = 298.15 ; Pressure coupling is on Pcoupl = berendsen tau_p = 2.0 compressibility = 4.6e-5 ref_p = 1.0 ; Generate velocites is on at 323.15 K. gen_vel = yes gen_temp= 298.15 gen_seed = 173529 Jinyao Wang wan...@ciac.jl.cn 2009-10-23 ___ 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 -- David van der Spoel, Ph.D., Professor of Biology Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. 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] scripts to generate topology CG
On Fri, Oct 23, 2009 at 4:14 PM, Justin A. Lemkul jalem...@vt.edu wrote: Francesco Pietra wrote: Hello Sunny: I had already generated a valid .itp file for my protein using seq2itp. That .itp works for both the protein itself and the protein graphically inserted into a bilayer. When I add graphically further water it does not work any more. I thought there is something else that manages water without putting it everywhere. That script does not help. In order to get a solution to your problem, I think you're going to have to explain your methodology more clearly, including command lines and actual error messages. How are you adding water graphically? Is genbox not working? Can you not simply grep for the number of water molecules, i.e.: grep W solvated.gro | wc -l and use that number in the topology? -Justin I'll organize to explain in more details. The methodology (all-atoms) is explained in a few papers of mine and supplementary material, for example: F. Pietra “ Docking and MD simulations of the interaction of the tarantula peptide psalmotoxin‑1 with ASIC1a channels using a homology model” J. Chem. Inf. Model. 2009, 49, 972-977. thanks francesco thanks francesco On Wed, Oct 21, 2009 at 3:46 PM, sunny mishra mishra.su...@gmail.com wrote: There is a seq2itp.pl script provided by martini folks in their website. You can get it from there. Sunny On Wed, Oct 21, 2009 at 9:42 AM, Francesco Pietra francesco.pie...@accademialucchese.it wrote: Hi: I am looking for scripts that generate topology in coarse grained. Thanks for indications. francesco pietra ___ 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-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-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 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing list gmx-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 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: Re: how to calculate the vaporation enthalpy of pure small organic compound (Justin A. Lemkul)
Dear Justin, Thank you for your help. I indeed didn't use the option -nmol 512. Jinyao Wang wrote: Hi gmx-users, I want to calcualted the the vaporation enthalpy of benzaldehyde I think that the the vaporation enthalpy is the sum of non-bond interacion among the benzaldehyde molecule. So I made a NPT system simulation including 512 benzaldehyde molecule. The following is the intermolecule nonbond interaction using the g_energy. LJ-(SR)= -21128.7 Kj/mol LJ-(LR)= -889.855 Kj/mol Coulomb-(SR)= -3884.6 Kj/mol Coul.-recip = -2261.51 Kj/mol the sum of non-bond interaction = LJ-(SR) + LJ-(LR) + Coulomb-(SR) + Coul.-recip = 28164.665 Kj/mol But the experimental value of he vaporation enthalpy = 50.3 Kj/mol I have no ideal that why they have so much different. Now I don't know how to solve it. Any suggestion will be appreciated. These are totals for the intermolecular energy of the system. I'm guessing you didn't use -nmol 512 to calculate these results? -Justin This following is my md.mdp file. title = fws cpp = /usr/bin/cpp constraints = all-bonds integrator = md dt = 0.002; ps ! nsteps = 50 ; total 1ns nstcomm = 1 nstxout = 500 nstvout = 0 nstfout = 0 nstlist = 10 ns_type = grid rlist = 1.0 coulombtype = PME rcoulomb= 1.0 vdwtype = cut-off rvdw= 1.4 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 6 ewald_rtol = 1e-5 optimize_fft= yes ; Berendsen temperature coupling is on in three groups Tcoupl = berendsen tau_t = 0.1 tc_grps = system ref_t = 298.15 ; Pressure coupling is on Pcoupl = berendsen tau_p = 2.0 compressibility = 4.6e-5 ref_p = 1.0 ; Generate velocites is on at 323.15 K. gen_vel = yes gen_temp= 298.15 gen_seed = 173529 � ���Jinyao Wang wan...@ciac.jl.cn ��2009-10-23 ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- ___ gmx-users mailing 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! End of gmx-users Digest, Vol 66, Issue 157 ** = = = = = = = = = = = = = = = = = = = = 致 礼！ Jinyao Wang wan...@ciac.jl.cn 2009-10-23 ___ 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
Fwd: [gmx-users] scripts to generate topology CG
-- Forwarded message -- From: Francesco Pietra francesco.pie...@accademialucchese.it Date: Fri, Oct 23, 2009 at 5:01 PM Subject: Re: [gmx-users] scripts to generate topology CG To: jalem...@vt.edu, Discussion list for GROMACS users gmx-users@gromacs.org On Fri, Oct 23, 2009 at 4:14 PM, Justin A. Lemkul jalem...@vt.edu wrote: Francesco Pietra wrote: Hello Sunny: I had already generated a valid .itp file for my protein using seq2itp. That .itp works for both the protein itself and the protein graphically inserted into a bilayer. When I add graphically further water it does not work any more. I thought there is something else that manages water without putting it everywhere. That script does not help. In order to get a solution to your problem, I think you're going to have to explain your methodology more clearly, including command lines and actual error messages. How are you adding water graphically? Is genbox not working? Can you not simply grep for the number of water molecules, i.e.: grep W solvated.gro | wc -l and use that number in the topology? I forgot to add that the graphic program uses the above grep command, giving the same number of W as the line command. The number of DCCP is diminished by those deleted in inserting the protein, but the grompp command complains that .gro does not matches .top. If no further water is added graphically, everything works. -Justin I'll organize to explain in more details. The methodology (all-atoms) is explained in a few papers of mine and supplementary material, for example: F. Pietra “ Docking and MD simulations of the interaction of the tarantula peptide psalmotoxin‑1 with ASIC1a channels using a homology model” J. Chem. Inf. Model. 2009, 49, 972-977. thanks francesco thanks francesco On Wed, Oct 21, 2009 at 3:46 PM, sunny mishra mishra.su...@gmail.com wrote: There is a seq2itp.pl script provided by martini folks in their website. You can get it from there. Sunny On Wed, Oct 21, 2009 at 9:42 AM, Francesco Pietra francesco.pie...@accademialucchese.it wrote: Hi: I am looking for scripts that generate topology in coarse grained. Thanks for indications. francesco pietra ___ 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-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-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 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing list gmx-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 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] scripts to generate topology CG
Francesco Pietra wrote: On Fri, Oct 23, 2009 at 4:14 PM, Justin A. Lemkul jalem...@vt.edu wrote: Francesco Pietra wrote: Hello Sunny: I had already generated a valid .itp file for my protein using seq2itp. That .itp works for both the protein itself and the protein graphically inserted into a bilayer. When I add graphically further water it does not work any more. I thought there is something else that manages water without putting it everywhere. That script does not help. In order to get a solution to your problem, I think you're going to have to explain your methodology more clearly, including command lines and actual error messages. How are you adding water graphically? Is genbox not working? Can you not simply grep for the number of water molecules, i.e.: grep W solvated.gro | wc -l and use that number in the topology? -Justin I'll organize to explain in more details. The methodology (all-atoms) is explained in a few papers of mine and supplementary material, for example: F. Pietra “ Docking and MD simulations of the interaction of the tarantula peptide psalmotoxin‑1 with ASIC1a channels using a homology model” J. Chem. Inf. Model. 2009, 49, 972-977. I read the methods there, and one of your own references therein, but it doesn't really help that much. I understand what you're aiming for, but atomistic system preparation in AMBER and coarse-grain system preparation in GROMACS is like comparing apples and oranges. Seeing details of successful methodology doesn't illuminate the problems you're currently having. I still don't know what you're trying to do in GROMACS that's causing a problem. Again, it would be helpful to see the commands you're issuing, and any other pertinent information (especially error messages, topology snippets, etc) to better diagnose your problem. If solvation is the issue, I maintain that genbox can do the job much like Leap does in AMBER. You may have to take a few tips from this page about adding water: http://www.gromacs.org/Documentation/How-tos/Membrane_Simulations -Justin thanks francesco thanks francesco On Wed, Oct 21, 2009 at 3:46 PM, sunny mishra mishra.su...@gmail.com wrote: There is a seq2itp.pl script provided by martini folks in their website. You can get it from there. Sunny On Wed, Oct 21, 2009 at 9:42 AM, Francesco Pietra francesco.pie...@accademialucchese.it wrote: Hi: I am looking for scripts that generate topology in coarse grained. Thanks for indications. francesco pietra ___ 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 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe
Re: Fwd: [gmx-users] scripts to generate topology CG
Francesco Pietra wrote: grep W solvated.gro | wc -l and use that number in the topology? I forgot to add that the graphic program uses the above grep command, I don't understand this statement. giving the same number of W as the line command. The number of DCCP is diminished by those deleted in inserting the protein, but the grompp command complains that .gro does not matches .top. If no further water is added graphically, everything works. This is where exact commands (in sequence) really help, or at least a stepwise procedure. Are you adding a protein into a box that contains DCCP+water, or are you inserting the protein into DCCP, then adding water? What is the exact error that grompp is giving you? That the number of coordinates don't match? atom names don't match? -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] How can measure the end-yo end distance of a peptide from the .xtc file
Dear all, I would like to get the distance information of the small peptide chain from the .xtc file, but the g_mindist seems can only get the distance information from one group to another. How I can get the end to end distance? I mean the distance between an end atom of the short chain to the other end atom? Thanks in advance. Cheers, Haifeng YUAN ___ 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] How can measure the end-yo end distance of a peptide from the .xtc file
haifeng YUAN wrote: Dear all, I would like to get the distance information of the small peptide chain from the .xtc file, but the g_mindist seems can only get the distance information from one group to another. How I can get the end to end distance? I mean the distance between an end atom of the short chain to the other end atom? g_dist with appropriate index groups. -Justin Thanks in advance. Cheers, Haifeng YUAN ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] how to stop duplicate atoms from being deleted
Thanks again for the help. I?ve given it a go but am not overly confident or exactly sure how I would translate this method to my system. This is because rather than having a chain with a well defined start and finish I have a giant covalent structure (like a web) where each silicon is tetrahedrally bound to oxygen (as in quartz). O? | ?O-Si-O ? | O? Here I describe my efforts so far. I have defined a monomer (my internal unit) as an SiO4 tetrahedra. Therefore each monomer would have to form 4 bonds with other monomers. I have defined my internal residue like this: ; Internal residue [ MCM_I ] [ atoms ] SISI1.280 1 O1O1 -0.640 1 O2O2 -0.640 1 O3O3 -0.640 1 O4O4 -0.640 1 [ bonds ] SIO1 SIO2 SIO3 SIO4 O1 -SI O2 -SI O3 +SI O4 +SI As an aside-This means that each residue is not neutral as the charges cancel out over the entire molecule and not over a single residue-I am not sure of the implications of this. To complicate matters, in my structure not all of the oxygens are bonded oxygens (i.e where each O is bonded to 2 silicons, some of the oxygens terminate in hydroxyl groups). This means that I have will have 3 types of terminal/starting chain 1. Si, O, O, OH 2. SI, O, OH, OH 3. SI, OH, OH, OH (the group which really does terminate) Here are my terminal and starting residues: ; terminal residue 1 (3OH groups) [ MCM_T1 ] [ atoms ] SISI 1.280 1 OH1OH1 -0.502 1 H1H1 0.206 1 OH2OH2 -0.502 1 H2H2 0.206 1 OH3OH3 -0.502 1 H3H3 0.206 1 O4O4-0.640 1 [ bonds ] SI OH1 SI OH2 SI OH3 SIO4 OH1 H1 OH2 H2 OH3 H3 O4 -SI ; terminal residue 2 (2 OH groups) [ MCM_T2 ] [ atoms ] SISI 1.280 1 OH1 OH1-0.502 1 H1H1 0.206 1 OH2 OH2-0.502 1 H2H2 0.206 1 O3O3-0.640 1 O4O4-0.640 1 [ bonds ] SI OH1 SI OH2 SIO3 SIO4 OH1 H1 OH2 H2 O3 -SI O4 -SI ; terminal residue 3 (1 OH group) [ MCM_T3 ] [ atoms ] SI SI 1.280 1 OH1 OH1-0.502 1 H1H1 0.206 1 O2O2-0.640 1 O3O3-0.640 1 O4O4-0.640 1 [ bonds ] SI OH1 SIO2 SIO3 SIO4 OH1H1 O2 -SI O3 -SI O4 -SI As each of these groups could equally be starting groups-I have defined them as such by changing the minus sign to a plus ; starting residue 1 [ MCM_S1 ] [ atoms ] SISI1.280 1 OH1OH1 -0.502 1 H1H1 0.206 1 OH2OH2 -0.502 1 H2H2 0.206 1 OH3OH3 -0.502 1 H3H3 0.206 1 O4O4-0.640 1 [ bonds ] SI OH1 SI OH2 SI OH3 SIO4 O4 +SI ; starting residue 2 [ MCM_T2 ] [ atoms ] SISI 1.280 1 OH1 OH1-0.502 1 H1H1 0.206 1 OH2 OH2-0.502 1 H2H2 0.206 1 O3O3-0.640 1 O4O4-0.640 1 [ bonds ] SI OH1 SI OH2 SIO3 SIO4 O3 +SI O4 +SI ; starting residue 3 [ MCM_T3 ] [ atoms ] SI SI 1.280 1 OH1 OH1-0.502 1 H1H1 0.206 1 O2O2-0.640 1 O3O3-0.640 1 O4O4-0.640 1 [ bonds ] SI OH1 SIO2 SIO3 SIO4 O2 +SI O3 +SI O4 +SI There are a few problems with this: 1. I don?t know how to go about splitting my large .pdb file into monomers. At the moment it is ordered by atomtype VMD doesn?t recognise my self- defined SiO2 tetrahedra as monomers so I can?t sort using that. There is no way I can do this manually by looking at the coordinates. 2. Looking at the terminal residue 1 for example, I have defined the only non-bonded oxygen as O4-however it could equally be O1, O2 or O3-this leads to a number of possible combinations of my terminal and internal residues. 3. There is in fact no such thing as a terminal residue (except in the case of Terminal residue 1 which is rare). It is more common to have a 2 OH groups on a silicon meaning the other oxygens bond to further residues. I can see how this method works nicely for a chain but having a four coordinate system really complicates things! I have run a very simple pdb file using pdb2gmx, the new .rtp file above and a handwritten .pdb file with 2 monomers. The result is that pdb2gmx is creating extra bonds between the Silicon of one monomer and the oxygen of the next meaning I am getting a 5-coordinate Silicon. Pdb2gmx doesn?t seem to be able to distinguish based on bond distances
Re: [gmx-users] how to stop duplicate atoms from being deleted
Jennifer Williams wrote: Thanks again for the help. I?ve given it a go but am not overly confident or exactly sure how I would translate this method to my system. This is because rather than having a chain with a well defined start and finish I have a giant covalent structure (like a web) where each silicon is tetrahedrally bound to oxygen (as in quartz). O? | ?O-Si-O ? | O? Here I describe my efforts so far. I have defined a monomer (my internal unit) as an SiO4 tetrahedra. Therefore each monomer would have to form 4 bonds with other monomers. I have defined my internal residue like this: ; Internal residue [ MCM_I ] [ atoms ] SISI1.280 1 O1O1 -0.640 1 O2O2 -0.640 1 O3O3 -0.640 1 O4O4 -0.640 1 [ bonds ] SIO1 SIO2 SIO3 SIO4 O1 -SI O2 -SI O3 +SI O4 +SI As an aside-This means that each residue is not neutral as the charges cancel out over the entire molecule and not over a single residue-I am not sure of the implications of this. To complicate matters, in my structure not all of the oxygens are bonded oxygens (i.e where each O is bonded to 2 silicons, some of the oxygens terminate in hydroxyl groups). This means that I have will have 3 types of terminal/starting chain 1. Si, O, O, OH 2. SI, O, OH, OH 3. SI, OH, OH, OH (the group which really does terminate) Here are my terminal and starting residues: ; terminal residue 1 (3OH groups) [ MCM_T1 ] [ atoms ] SISI 1.280 1 OH1OH1 -0.502 1 H1H1 0.206 1 OH2OH2 -0.502 1 H2H2 0.206 1 OH3OH3 -0.502 1 H3H3 0.206 1 O4O4-0.640 1 [ bonds ] SI OH1 SI OH2 SI OH3 SIO4 OH1 H1 OH2 H2 OH3 H3 O4 -SI ; terminal residue 2 (2 OH groups) [ MCM_T2 ] [ atoms ] SISI 1.280 1 OH1 OH1-0.502 1 H1H1 0.206 1 OH2 OH2-0.502 1 H2H2 0.206 1 O3O3-0.640 1 O4O4-0.640 1 [ bonds ] SI OH1 SI OH2 SIO3 SIO4 OH1 H1 OH2 H2 O3 -SI O4 -SI ; terminal residue 3 (1 OH group) [ MCM_T3 ] [ atoms ] SI SI 1.280 1 OH1 OH1-0.502 1 H1H1 0.206 1 O2O2-0.640 1 O3O3-0.640 1 O4O4-0.640 1 [ bonds ] SI OH1 SIO2 SIO3 SIO4 OH1H1 O2 -SI O3 -SI O4 -SI As each of these groups could equally be starting groups-I have defined them as such by changing the minus sign to a plus ; starting residue 1 [ MCM_S1 ] [ atoms ] SISI1.280 1 OH1OH1 -0.502 1 H1H1 0.206 1 OH2OH2 -0.502 1 H2H2 0.206 1 OH3OH3 -0.502 1 H3H3 0.206 1 O4O4-0.640 1 [ bonds ] SI OH1 SI OH2 SI OH3 SIO4 O4 +SI ; starting residue 2 [ MCM_T2 ] [ atoms ] SISI 1.280 1 OH1 OH1-0.502 1 H1H1 0.206 1 OH2 OH2-0.502 1 H2H2 0.206 1 O3O3-0.640 1 O4O4-0.640 1 [ bonds ] SI OH1 SI OH2 SIO3 SIO4 O3 +SI O4 +SI ; starting residue 3 [ MCM_T3 ] [ atoms ] SI SI 1.280 1 OH1 OH1-0.502 1 H1H1 0.206 1 O2O2-0.640 1 O3O3-0.640 1 O4O4-0.640 1 [ bonds ] SI OH1 SIO2 SIO3 SIO4 O2 +SI O3 +SI O4 +SI There are a few problems with this: 1.I don?t know how to go about splitting my large .pdb file into monomers. At the moment it is ordered by atomtype VMD doesn?t recognise my self- defined SiO2 tetrahedra as monomers so I can?t sort using that. There is no way I can do this manually by looking at the coordinates. 2.Looking at the terminal residue 1 for example, I have defined the only non-bonded oxygen as O4-however it could equally be O1, O2 or O3-this leads to a number of possible combinations of my terminal and internal residues. 3.There is in fact no such thing as a terminal residue (except in the case of Terminal residue 1 which is rare). It is more common to have a 2 OH groups on a silicon meaning the other oxygens bond to further residues. I can see how this method works nicely for a chain but having a four coordinate system really complicates things! I have run a very simple pdb file using pdb2gmx, the new .rtp file above and a handwritten .pdb file with 2 monomers. The result is that pdb2gmx is creating extra bonds between the Silicon of one monomer and the oxygen of the next meaning I am getting a 5-coordinate Silicon. Pdb2gmx doesn?t seem to be able to distinguish based on bond
Re: [gmx-users] how to stop duplicate atoms from being deleted
Justin A. Lemkul wrote: I can see how this rapidly becomes difficult :) I don't believe that pdb2gmx can handle such multi-directional bonding, since the residues that are connected are not necessarily numerically sequential. I should amend this statement (typing quicker than the brain can keep up!) - It is not that pdb2gmx cannot handle multi-directional bonding, it is moreso that I don't think it cannot be done using the +/- convention of the .rtp files. Using specbond.dat, as I suggested before, should be a viable alternative. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] positional restraint
Hi, I was wondering if it would be possible to apply positional restraint to an atom w.r.t an arbitrary coordinate. Say for eg. I want to constrain the distance between an atom and the origin(0,0,0) during MD. Is it possible to do that in GROMACS. Thanks Krishna ___ 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] Which membrane result is more reliable?
Hello Justin, You helped me before, and I am grateful for that. So basically my summer research had ended up with the following results: I have included my *.ipt files this message is long. *My question: 1)why once simulation is giving me stable aplha-helix and other is not if membranes are similar and conditions kept constant. * 2) Which result to use, most probale. Does lipid density might of affected the stability? -200ns Simulation of the same peptide in the DMPC only box and in DMPC/DMPE box [1:1 ratio] but results are different and I want to ask why as this data will go as part of the paper. *System:* peptide that is placed on TOP of the membrane, interacting with lipids (no inserted into the membrane, but floating on top) and above there are water molecules * DMPC membrane simulation - STABLE Peptide Helix, no uncoiling:* - 248 DMPC molecules -Box 9.03 x 9.03 x 10.15 as found at the bottom of gro file (I think this dimensions are nm units?) - Threfore I calculated that Area per Lipid is only: 2facesx90.3^2 A^2/248DMPC = 65.75 A^2/lipid which is low - When I was using InflatGro(which I modified to be much more friendly and accepts 2 lipids) to check the lipid density the values were: ___ Input *.gro file to shrink or expand:dmpc.gro Enter membrane re-scaling factor (default=0.95):*1* Enter Lipid#1 name (e.g. DMPC):DMPC Enter Lipid#2 name (e.g. DMPE) otherwise ENTER: For spacial overlap estimation between lipids... Please enter distance cutoff value between lipids in A(default = 14):14 Output file name(e.g.'inflated.gro'):rm.gro Gridsize for area per lipid calculations in A(default = 5):5 TOTAL Area per protein: 1.5 nm^2 or 150.00 A^2 *TOTAL Area per lipid: 0.67 nm^2 or 67.26 A^2* -- why different from prev. calculation, slightly smaller? Area per protein, upper half: 0.000 nm^2or 0.000 A^2 Area per lipid, upper leaflet : 0.632 nm^2 or 63.210 A^2 Area per protein, lower half: 1.50 nm^2or 150.00 A^2 Area per lipid, lower leaflet : 0.73 nm^2 or 73.43 A^2 ___ Total Energy: Statistics over 82987501 steps [ 109970.0078 thru 275945. ps ], 1 data sets All averages are exact over 82987501 steps Energy Average RMSD Fluct. Drift Tot-Drift --- *Total Energy-891474 *kJ/mol 1132.811131.48 -0.00114556 -190.135 T-Protein 309.844 25.330725.3304 -2.37026e-06 -0.393404 *DMPE/DMPC membrane simulation - Becomes UNSTABLE after 100ns simulation time * - 93 DMPC and 93 DMPE molecules -Density: 2faces*68.2*68.2 / 186 lipids = 50 A^2/lipid - InflateGro results: _ TOTAL Area per protein: 0 nm^2 or 0.00 A^2 *TOTAL Area per lipid: 0.49 nm^2 or 48.52 A^2* again smaller? Area per protein, upper half: 0.000 nm^2or 0.000 A^2 Area per lipid, upper leaflet : 0.485 nm^2 or 48.517 A^2 Area per protein, lower half: 0.00 nm^2or 0.00 A^2 Area per lipid, lower leaflet : 0.49 nm^2 or 48.52 A^2 Writing Area per lipid... Done! ___ DMPC: has 46 atoms and DMPE: has 46 atoms Total Energy: Statistics over 10001 steps [ 0. thru 20.0156 ps ], 1 data sets All averages are exact over 10001 steps Energy Average RMSD Fluct. Drift Tot-Drift --- *Total Energy-477439 kJ/mol * 839.231790.016 -0.0049046-980.92 T-Protein_DMPC_DMPE 309.657 3.27193.27189 -9.55346e-08 -0.0191069 I used the same *.mdp file *I used following dmpe.ipt and dmpc files * attached that to my 1st impression are identical ___ 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] Which membrane result is more reliable?
Kirill Bessonov wrote: Hello Justin, You helped me before, and I am grateful for that. So basically my summer research had ended up with the following results: I have included my *.ipt files this message is long. *My question: 1)why once simulation is giving me stable aplha-helix and other is not if membranes are similar and conditions kept constant. * 2) Which result to use, most probale. Does lipid density might of affected the stability? -200ns Simulation of the same peptide in the DMPC only box and in DMPC/DMPE box [1:1 ratio] but results are different and I want to ask why as this data will go as part of the paper. There is nothing that suggests to me you should expect similar results under these different conditions. Many proteins will behave wildly differently in the presence of different headgroup charges and chemical functional groups. As for DMPC, the quaternary amine group is capable of electrostatic interactions, while DMPE can participate in hydrogen bonding as well as electrostatic interactions, within the lipids and also with the protein. I can think of one example immediately where PE and PC headgroups induce structural changes in proteins, I'm sure there are more. *System:* peptide that is placed on TOP of the membrane, interacting with lipids (no inserted into the membrane, but floating on top) and above there are water molecules _* DMPC membrane simulation - STABLE Peptide Helix, no uncoiling:*_ - 248 DMPC molecules -Box 9.03 x 9.03 x 10.15 as found at the bottom of gro file (I think this dimensions are nm units?) Yes, per Chapter 2 in the GROMACS manual, the standard unit of length is nm. - Threfore I calculated that Area per Lipid is only: 2facesx90.3^2 A^2/248DMPC = 65.75 A^2/lipid which is low Can you guarantee that no part of your protein occupies this lateral space? If the protein is interacting with the lipids, I would think that this calculation is inappropriate. - When I was using InflatGro(which I modified to be much more friendly and accepts 2 lipids) to check the lipid density the values were: The InflateGRO code (by its own admission) also overestimates area per lipid. I would not use these data at face value. Might I put in a plug for a program developed in our own lab, designed for these exact situations: http://www.bevanlab.biochem.vt.edu/GridMAT-MD/ snip I used the same *.mdp file *I used following dmpe.ipt and dmpc files * attached that to my 1st impression are identical There are no attachments. I don't know what you mean by claiming they are identical. PE and PC lipids behave differently. -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 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] positional restraint
krishnakumar wrote: Hi, I was wondering if it would be possible to apply positional restraint to an atom w.r.t an arbitrary coordinate. Say for eg. I want to constrain the distance between an atom and the origin(0,0,0) during MD. Is it possible to do that in GROMACS. I don't believe there is a way to implement an absolute restraint, nor do I immediately see why it would be meaningful. You could, however, build your system so the atom of interest is placed appropriately and simply use position restraints on it. -Justin Thanks Krishna ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: Re: how to calculate the vaporation enthalpy of pure small organic compound (David van der Spoel)
Hi David, Thank you for your help. I am very sorry to trouble you. I have know your means that the gas-phase energy should be considered. But I am confused that you said the gas-phase energy (with com removed) and add kT. What is the gas-phase energy (with com removed) and Could you talk about the details? Jinyao Wang wrote: Hi gmx-users, I want to calcualted the the vaporation enthalpy of benzaldehyde I think that the the vaporation enthalpy is the sum of non-bond interacion among the benzaldehyde molecule.So I made a NPT system simulation including 512 benzaldehyde molecule. The following is the intermolecule nonbond interaction using the g_energy. LJ-(SR)= -21128.7 Kj/mol LJ-(LR)= -889.855 Kj/mol Coulomb-(SR)= -3884.6 Kj/mol Coul.-recip = -2261.51 Kj/mol the sum of non-bond interaction = LJ-(SR) + LJ-(LR) + Coulomb-(SR) + Coul.-recip = 28164.665 Kj/mol But the experimental value of he vaporation enthalpy = 50.3 Kj/mol I have no ideal that why they have so much different. Now I don't know how to solve it. Any suggestion will be appreciated. These are totals for the intermolecular energy of the system. I'm guessing you didn't use -nmol 512 to calculate these results? And then subtract the gas-phase energy (with com removed) and add kT. Jinyao Wang wan...@ciac.jl.cn 2009-10-24 ___ 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] Does GMX compute coulomb interaction between oxygen and hydrogen in SPC water model?
Hi all gromcas users: In SPC water model, it only has oxygen-oxygen VDW interactons. So is it the same with coulomb interatctions? Thanks for any advice in advance! 2009-10-24 Ji Xu The State Key Laboratory of Multiphase Complex System Institute of Process Engineering Chinese Academy of Sciences Beijing 100190, China Tel.: +86 10 8262 3713-804 ___ 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] Does GMX compute coulomb interaction between oxygen and hydrogen in SPC water model?
xuji wrote: Hi all gromcas users: In SPC water model, it only has oxygen-oxygen VDW interactons. So is it the same with coulomb interatctions? No, otherwise it would be a one-point water model. All SPC water atoms have partial charges - see spc.itp. 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
