Antw: [gmx-users] How to suppress the error X particles communicated to PME node Y are more than a cell length out of the domain decomposition cell of their charge group
Hello, Have you also tried this simulation with a velocity rescaling thermostat in the equilibration period? Could it be that it then would work better? Bests, Emanuel WU Yanbin 02.12.10 6.16 Uhr Dear GMXers, I'm running a simulation of water contact angle measurement on top of graphite surface. Initially a water cubic box is placed on two-layer graphite surface with the rest of the box being vacuum. The water droplet is relaxed during the simulation to develop a spherical shape. An error of X particles communicated to PME node Y are more than a cell length out of the domain decomposition cell of their charge group was encountered. And I have read the suggested solutions at the link below http://www.gromacs.org/Documentation/Errors#X_particles_communicated_to_PME_node_Y_are_more_than_a_cell_length_out_of_the_domain_decomposition_cell_of_their_charge_group. I guess the reason for this error in my case is because of the vacuum such that the water molecules at the boundary of the droplet can move fast. I have check the trajectory and the simulation is OK. For this situation, is there a way of suppressing this error? Or what else can I do? PS: the GROMACS version I'm using is GROMACS4.5. Thank you. Best, Yanbin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Fwd: lateral diffusion coefficients on a spherical surface
Hi, I am forwarding on a message on behalf of one of my colleagues who is having problems sending messages to the list. Please take a look his message and see if you can help him with his problem. Thank you Tom Piggot Original Message Subject:lateral diffusion coefficients on a spherical surface Date: Thu, 2 Dec 2010 08:05:36 + From: Daniel dah1...@soton.ac.uk To: Piggot T. t.pig...@soton.ac.uk Dear Gromacs users, I would like to calculate some lateral diffusion coefficients of molecules on a spherical surface. I realise that there is no gromacs tool that can do this, but I was wondering if there might be a clever way to edit the code for g_msd? I am currently using Gromacs version 4.0.7. Firstly, I would like to calculate the arc length – the approximate displacement across the surface of the sphere, instead of the linear displacement. Secondly, I would like to remove any angular movement resulting from the rotation of the whole sphere. I realise that there may be a way to do this during the simulation using the com_mode set to angular, but is there a way to post process a trajectory to remove the rotation of the whole sphere? Would post processing of the simulation trajectory introduce errors? Thank you very much for your help, Daniel -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Restraining water
2010/12/2 Mark Abraham mark.abra...@anu.edu.au On 2/12/2010 12:51 PM, Guido Polles wrote: Hi, I know it looks a little bit strange, but i was trying to restrain just some water in my system. Now, if i put something like [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 I put restraints on all the molecules. Yes, that directive will pertain to all the molecules that have that [ moleculetype ]. I'm not sure if you only want position restraints on some of your water molecules. I thought about a turnaround, just making a second water molecule type, but now complains about using more than one settle type. Is there any other way to do it? Guido, You may find this thread useful: http://lists.gromacs.org/pipermail/gmx-users/2010-September/054087.html And if I follow the Suggestion: change the least use settle constraints into 3 normal constraints I have to worry about some kind of huge loss in performance? I would expect the non-settle waters to use the solvent-optimized loops in the normal way, so there should be no difference in execution time between the unrestrained all-settle simulation and the partly-restrained party-settled simulation. Obviously, this is straightforward to test. 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/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- David Rodríguez Díaz, PhD Student Fundación Pública Galega de Medicina Xenómica (SERGAS) Web page: http://webspersoais.usc.es/persoais/david.rodriguez.diaz -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] add a new force field to the pdb2gmx list
yes, I lost a forcefield.itp file. 2010/12/1 Mark Abraham mark.abra...@anu.edu.au On 1/12/2010 3:55 PM, Jia Haitao wrote: No, I did not miss any files in direction .ff. I even add a ffpolycg.itp in ../$GMXLIB. Is there any file like FF.dat ? See pdb2gmx -h Mark 2010/12/1 Mark Abraham mark.abra...@anu.edu.au On 1/12/2010 3:17 PM, Jia Haitao wrote: Dear all, I have constructed a new CG force field named polycg, and added them to direction ..$GMXLIB/polycg.ff. Can anybody tell me how to add my new force field to gromacs default force field list, in case I can use it to convert pdb files in program pdb2gmx. My gromacs version is 4.5. There is not FF.dat file in direction $GMXLIB any more. I will be very appreciate for your help. Look at the contents for the other force fields. There's probably something you don't have, like forcefield.doc 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/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] How to suppress the error X particles communicated to PME node Y are more than a cell length out of the domain decomposition cell of their charge group
On Dec 2, 2010, at 6:16 AM, WU Yanbin wrote: Dear GMXers, I'm running a simulation of water contact angle measurement on top of graphite surface. Initially a water cubic box is placed on two-layer graphite surface with the rest of the box being vacuum. The water droplet is relaxed during the simulation to develop a spherical shape. An error of X particles communicated to PME node Y are more than a cell length out of the domain decomposition cell of their charge group was encountered. And I have read the suggested solutions at the link below http://www.gromacs.org/Documentation/Errors#X_particles_communicated_to_PME_node_Y_are_more_than_a_cell_length_out_of_the_domain_decomposition_cell_of_their_charge_group. I guess the reason for this error in my case is because of the vacuum such that the water molecules at the boundary of the droplet can move fast. I have check the trajectory and the simulation is OK. For this situation, is there a way of suppressing this error? Or what else can I do? If the system is small enough, you can run it on a single core and the problem cannot occur. You could also try to use particle decomposition (-pd) instead of domain decomposition. Or use less domains, i.e. less cores in total or at least less PP nodes if you use PME/PP splitting. This will at least reduce the probability for the problem to occur. Carsten PS: the GROMACS version I'm using is GROMACS4.5. Thank you. Best, Yanbin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Allocation memory failure with g_msd (version 4.5.X)
Hi all. I found a memory allocation problem when using g_msd in verions 4.5.1 and higher when the option -mol is enabled. Here you have the command line input: $ g_msd -f DPPC_run -s DPPC_run -n -lateral z -o D_mol -b 1 -mol And the error message: Program g_msd, VERSION 4.5.3 Source code file: smalloc.c, line: 214 Fatal error: Not enough memory. Failed to realloc 8192 bytes for stats-y, stats-y=0x0 (called from file gmx_statistics.c, line 110) As monitored with top command, thats actually what is happening: program start to take a lot of memory from buffer until it crash. However this is not the case when the option -mol is not request or when using previous versions (even with -mol option). Am I doing something wrong? Is there anything extra to care about when submitting g_msd from versions 4.5.X? Thanks for your attention. Javier -- Javier CEREZO BASTIDA Estudiante de Doctorado - Dpto. Química-Física Universidad de Murcia 30100 MURCIA (España) Tlf.(+34)868887434 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: individual lateral diffusion coefficients
I want to add that the MSD as a function of time (msd.xvg file) looks completely linear Greetings, Ángel Piñeiro. On Thu, 2010-12-02 at 12:45 +0100, Ángel Piñeiro wrote: Dear all, I aim to calculate the lateral diffusion coefficients of lipids as a function of the distance to a membrane protein using the Martini force field. For this I guess I could use the diff_mol.xvg output file of the g_msd command which provides the list of diffusion coefficients for each lipid (I guess the lipids are ordered as in the trajectory file). Then I would calculate the protein-lipid distance for each lipid and I would generate the diffusion vs distance file. Before starting the calculations on the membrane protein system I tested the g_msd command on a DPPC bilayer. In my bilayer simulation I removed the COM of lipids and water separately. Before analyzing it I removed jumps over the box boundaries using trjconv -pbc nojump and I created a index file with the PO4 atoms as a new group. Then I executed the following command: g_msd -s topol.tpr -f trajnojump.xtc -n p.ndx -lateral z -rmcomm from which I get the following output: D[ PO4] 0.0958 (+/- 0.0135) 1e-5 cm^2/s I think the value is not crazy for DPPC at 323 K using Martini... but I noticed that the D values for the independent lipids reported in the diff_mol.xvg file range from 0.0021959 to 0.482909 cm^2/s. If the differences are so high for a single lipid bilayer I suspect that I will not observe significant differences as a function of the distance to the protein in my simulations of the whole system... probably I am doing something wrong¿? Thanks for any advice Ángel Piñeiro. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] individual lateral diffusion coefficients
Dear all, I aim to calculate the lateral diffusion coefficients of lipids as a function of the distance to a membrane protein using the Martini force field. For this I guess I could use the diff_mol.xvg output file of the g_msd command which provides the list of diffusion coefficients for each lipid (I guess the lipids are ordered as in the trajectory file). Then I would calculate the protein-lipid distance for each lipid and I would generate the diffusion vs distance file. Before starting the calculations on the membrane protein system I tested the g_msd command on a DPPC bilayer. In my bilayer simulation I removed the COM of lipids and water separately. Before analyzing it I removed jumps over the box boundaries using trjconv -pbc nojump and I created a index file with the PO4 atoms as a new group. Then I executed the following command: g_msd -s topol.tpr -f trajnojump.xtc -n p.ndx -lateral z -rmcomm from which I get the following output: D[ PO4] 0.0958 (+/- 0.0135) 1e-5 cm^2/s I think the value is not crazy for DPPC at 323 K using Martini... but I noticed that the D values for the independent lipids reported in the diff_mol.xvg file range from 0.0021959 to 0.482909 cm^2/s. If the differences are so high for a single lipid bilayer I suspect that I will not observe significant differences as a function of the distance to the protein in my simulations of the whole system... probably I am doing something wrong¿? Thanks for any advice Ángel Piñeiro. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] proton proton transfer
Dear gromacs users, I want to simulate proton transfer between water and another small molecule in gromacs. In the end I should have the velosity of proton proton exchange. Please can you advice me which method is better to use for this in gromacs. I read about umbrella sampling, but may be there is other techniques? Yours sincerely, Olga -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: individual lateral diffusion coefficients
Hello Ángel. Well, there are a some things that I don't understand about your calculation, but might be just a problem of mine. Here you have my comments: 1. How do you get the diff_mol.xvg file if you are not using -mol in your command line input (and you index file has broken molecules). 2. Why do you select just an atom to calculate the diffusion? According to Wolhert and Edholm (JCP, 125, 204703) the MSD for all lipids atoms reach the same slope, so I guess using them all could improve sampling (I'm not sure). 3. I think that reprocessing of your trajectory to remove jumps is no longer needed (I got the same results in a recent test using version 4.5.1). 4. What I would do to calculate D as funtion to the distance to the membrane protein is generate different index files containing lipids according to this distance (and hoping they don't move a lot during the simulation) and run different msd calculations. I think I have read in the mailing list about a script to make such a selection regarding distances to construct the index file or just make your own one. Good luck Javier El 02/12/10 12:50, Ángel Piñeiro escribió: I want to add that the MSD as a function of time (msd.xvg file) looks completely linear Greetings, Ángel Piñeiro. On Thu, 2010-12-02 at 12:45 +0100, Ángel Piñeiro wrote: Dear all, I aim to calculate the lateral diffusion coefficients of lipids as a function of the distance to a membrane protein using the Martini force field. For this I guess I could use the diff_mol.xvg output file of the g_msd command which provides the list of diffusion coefficients for each lipid (I guess the lipids are ordered as in the trajectory file). Then I would calculate the protein-lipid distance for each lipid and I would generate the diffusion vs distance file. Before starting the calculations on the membrane protein system I tested the g_msd command on a DPPC bilayer. In my bilayer simulation I removed the COM of lipids and water separately. Before analyzing it I removed jumps over the box boundaries using trjconv -pbc nojump and I created a index file with the PO4 atoms as a new group. Then I executed the following command: g_msd -s topol.tpr -f trajnojump.xtc -n p.ndx -lateral z -rmcomm from which I get the following output: D[ PO4] 0.0958 (+/- 0.0135) 1e-5 cm^2/s I think the value is not crazy for DPPC at 323 K using Martini... but I noticed that the D values for the independent lipids reported in the diff_mol.xvg file range from 0.0021959 to 0.482909 cm^2/s. If the differences are so high for a single lipid bilayer I suspect that I will not observe significant differences as a function of the distance to the protein in my simulations of the whole system... probably I am doing something wrong¿? Thanks for any advice Ángel Piñeiro. -- Javier CEREZO BASTIDA Estudiante de Doctorado - Dpto. Química-Física Universidad de Murcia 30100 MURCIA (España) Tlf.(+34)868887434 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] proton proton transfer
Olga Ivchenko wrote: Dear gromacs users, I want to simulate proton transfer between water and another small molecule in gromacs. In the end I should have the velosity of proton proton exchange. Please can you advice me which method is better to use for this in gromacs. I read about umbrella sampling, but may be there is other techniques? You can't do this with standard MD. Bonds cannot break and re-form in a classical force field. You might be able to do accomplish it with QM, however, but in that case you need to be looking outside of Gromacs. -Justin Yours sincerely, Olga -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: individual lateral diffusion coefficients
Hi Javier 1.- you are right! the diff_mol.xvg file I reported was from a previous attempt in which I used the whole lipid molecules with the -mol option on, instead of the PO4 beads with -mol off. Sorry for this confusion 2.- As I said above, I did attempts using both the whole molecule and the PO4 beads. Yes I saw the figure 6 in the Wolhert Edholm's paper but I read in several other references that the calculation is more accurate by using only the P atom... what makes sense to me mainly for the lipids which are in contact with proteins 3.- I agree that removing jumps does not change anything. I decided to give this information in my message to avoid a reply saying try to remove jumps ;) 4.- Yes I agree that I could do the calculation by creating an index for each lipid... I guess that is the safest way to proceed... Thanks for your reply! Ángel. On Thu, 2010-12-02 at 13:30 +0100, Javier Cerezo wrote: Hello Ángel. Well, there are a some things that I don't understand about your calculation, but might be just a problem of mine. Here you have my comments: 1. How do you get the diff_mol.xvg file if you are not using -mol in your command line input (and you index file has broken molecules). 2. Why do you select just an atom to calculate the diffusion? According to Wolhert and Edholm (JCP, 125, 204703) the MSD for all lipids atoms reach the same slope, so I guess using them all could improve sampling (I'm not sure). 3. I think that reprocessing of your trajectory to remove jumps is no longer needed (I got the same results in a recent test using version 4.5.1). 4. What I would do to calculate D as funtion to the distance to the membrane protein is generate different index files containing lipids according to this distance (and hoping they don't move a lot during the simulation) and run different msd calculations. I think I have read in the mailing list about a script to make such a selection regarding distances to construct the index file or just make your own one. Good luck Javier El 02/12/10 12:50, Ángel Piñeiro escribió: I want to add that the MSD as a function of time (msd.xvg file) looks completely linear Greetings, Ángel Piñeiro. On Thu, 2010-12-02 at 12:45 +0100, Ángel Piñeiro wrote: Dear all, I aim to calculate the lateral diffusion coefficients of lipids as a function of the distance to a membrane protein using the Martini force field. For this I guess I could use the diff_mol.xvg output file of the g_msd command which provides the list of diffusion coefficients for each lipid (I guess the lipids are ordered as in the trajectory file). Then I would calculate the protein-lipid distance for each lipid and I would generate the diffusion vs distance file. Before starting the calculations on the membrane protein system I tested the g_msd command on a DPPC bilayer. In my bilayer simulation I removed the COM of lipids and water separately. Before analyzing it I removed jumps over the box boundaries using trjconv -pbc nojump and I created a index file with the PO4 atoms as a new group. Then I executed the following command: g_msd -s topol.tpr -f trajnojump.xtc -n p.ndx -lateral z -rmcomm from which I get the following output: D[ PO4] 0.0958 (+/- 0.0135) 1e-5 cm^2/s I think the value is not crazy for DPPC at 323 K using Martini... but I noticed that the D values for the independent lipids reported in the diff_mol.xvg file range from 0.0021959 to 0.482909 cm^2/s. If the differences are so high for a single lipid bilayer I suspect that I will not observe significant differences as a function of the distance to the protein in my simulations of the whole system... probably I am doing something wrong¿? Thanks for any advice Ángel Piñeiro. -- Javier CEREZO BASTIDA Estudiante de Doctorado - Dpto. Química-Física Universidad de Murcia 30100 MURCIA (España) Tlf.(+34)868887434 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: individual lateral diffusion coefficients
Hi Ángel Can you provide a citation about the use of only PO4 atoms to calculate the diffusion constant? Is it always recommended or just with CG simulations? I'm also working on diffusion calculation and that will be interesting. By the way, regarding the index files I mentioned, it might be better to have a group of lipids that are at a certain distance from the protein in the same index, again to improve sampling (maybe this is not a way to improve sampling, I don't know). Thanks Javier El 02/12/10 13:56, Ángel Piñeiro escribió: Hi Javier 1.- you are right! the diff_mol.xvg file I reported was from a previous attempt in which I used the whole lipid molecules with the -mol option on, instead of the PO4 beads with -mol off. Sorry for this confusion 2.- As I said above, I did attempts using both the whole molecule and the PO4 beads. Yes I saw the figure 6 in the Wolhert Edholm's paper but I read in several other references that the calculation is more accurate by using only the P atom... what makes sense to me mainly for the lipids which are in contact with proteins 3.- I agree that removing jumps does not change anything. I decided to give this information in my message to avoid a reply saying try to remove jumps ;) 4.- Yes I agree that I could do the calculation by creating an index for each lipid... I guess that is the safest way to proceed... Thanks for your reply! Ángel. On Thu, 2010-12-02 at 13:30 +0100, Javier Cerezo wrote: Hello Ángel. Well, there are a some things that I don't understand about your calculation, but might be just a problem of mine. Here you have my comments: 1. How do you get the diff_mol.xvg file if you are not using -mol in your command line input (and you index file has broken molecules). 2. Why do you select just an atom to calculate the diffusion? According to Wolhert and Edholm (JCP, 125, 204703) the MSD for all lipids atoms reach the same slope, so I guess using them all could improve sampling (I'm not sure). 3. I think that reprocessing of your trajectory to remove jumps is no longer needed (I got the same results in a recent test using version 4.5.1). 4. What I would do to calculate D as funtion to the distance to the membrane protein is generate different index files containing lipids according to this distance (and hoping they don't move a lot during the simulation) and run different msd calculations. I think I have read in the mailing list about a script to make such a selection regarding distances to construct the index file or just make your own one. Good luck Javier El 02/12/10 12:50, Ángel Piñeiro escribió: I want to add that the MSD as a function of time (msd.xvg file) looks completely linear Greetings, Ángel Piñeiro. On Thu, 2010-12-02 at 12:45 +0100, Ángel Piñeiro wrote: Dear all, I aim to calculate the lateral diffusion coefficients of lipids as a function of the distance to a membrane protein using the Martini force field. For this I guess I could use the diff_mol.xvg output file of the g_msd command which provides the list of diffusion coefficients for each lipid (I guess the lipids are ordered as in the trajectory file). Then I would calculate the protein-lipid distance for each lipid and I would generate the diffusion vs distance file. Before starting the calculations on the membrane protein system I tested the g_msd command on a DPPC bilayer. In my bilayer simulation I removed the COM of lipids and water separately. Before analyzing it I removed jumps over the box boundaries using trjconv -pbc nojump and I created a index file with the PO4 atoms as a new group. Then I executed the following command: g_msd -s topol.tpr -f trajnojump.xtc -n p.ndx -lateral z -rmcomm from which I get the following output: D[ PO4] 0.0958 (+/- 0.0135) 1e-5 cm^2/s I think the value is not crazy for DPPC at 323 K using Martini... but I noticed that the D values for the independent lipids reported in the diff_mol.xvg file range from 0.0021959 to 0.482909 cm^2/s. If the differences are so high for a single lipid bilayer I suspect that I will not observe significant differences as a function of the distance to the protein in my simulations of the whole system... probably I am doing something wrong¿? Thanks for any advice Ángel Piñeiro. -- Javier CEREZO BASTIDA Estudiante de Doctorado - Dpto. Química-Física Universidad de Murcia 30100 MURCIA (España) Tlf.(+34)868887434 -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Javier CEREZO BASTIDA Estudiante de
Re: [gmx-users] proton proton transfer
Thnaks, Justin. Probably CHARMM is suitable for this. 2010/12/2 Justin A. Lemkul jalem...@vt.edu Olga Ivchenko wrote: Dear gromacs users, I want to simulate proton transfer between water and another small molecule in gromacs. In the end I should have the velosity of proton proton exchange. Please can you advice me which method is better to use for this in gromacs. I read about umbrella sampling, but may be there is other techniques? You can't do this with standard MD. Bonds cannot break and re-form in a classical force field. You might be able to do accomplish it with QM, however, but in that case you need to be looking outside of Gromacs. -Justin Yours sincerely, Olga -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] proton proton transfer
Hi Olga, It's not straightforward in CHARMM as well. One method is to use conjugate peak refinement, but this will only get you the potential energy surface, but there's also a force field made by Meuwly for dealing with proton transfer IIRC. Depending on the system size, you may want to use QM/MM (implemented in Gromacs) or simulate your system with a DFT-based 'on semi-empricial code. Ran Ran Friedman Biträdande Lektor (Assistant Professor) Linnaeus University School of Natural Sciences 391 82 Kalmar, Sweden Norrgård, room 328d +46 480 446 290 Telephone +46 76 207 8763 Mobile ran.fried...@lnu.se http://lnu.se/research-groups/computational-chemistry-and-biochemistry-group?l=en From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of Olga Ivchenko [olga.ivche...@gmail.com] Sent: 02 December 2010 14:59 To: jalem...@vt.edu; Discussion list for GROMACS users Subject: Re: [gmx-users] proton proton transfer Thnaks, Justin. Probably CHARMM is suitable for this. 2010/12/2 Justin A. Lemkul jalem...@vt.edumailto:jalem...@vt.edu Olga Ivchenko wrote: Dear gromacs users, I want to simulate proton transfer between water and another small molecule in gromacs. In the end I should have the velosity of proton proton exchange. Please can you advice me which method is better to use for this in gromacs. I read about umbrella sampling, but may be there is other techniques? You can't do this with standard MD. Bonds cannot break and re-form in a classical force field. You might be able to do accomplish it with QM, however, but in that case you need to be looking outside of Gromacs. -Justin Yours sincerely, Olga -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.eduhttp://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.orgmailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.orgmailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] proton proton transfer
Sorry for the typo below. DFT based *or* semi empirical code. From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of Ran Friedman Sent: 02 December 2010 15:01 To: Discussion list for GROMACS users Subject: RE: [gmx-users] proton proton transfer Hi Olga, It's not straightforward in CHARMM as well. One method is to use conjugate peak refinement, but this will only get you the potential energy surface, but there's also a force field made by Meuwly for dealing with proton transfer IIRC. Depending on the system size, you may want to use QM/MM (implemented in Gromacs) or simulate your system with a DFT-based 'on semi-empricial code. Ran Ran Friedman Biträdande Lektor (Assistant Professor) Linnaeus University School of Natural Sciences 391 82 Kalmar, Sweden Norrgård, room 328d +46 480 446 290 Telephone +46 76 207 8763 Mobile ran.fried...@lnu.se http://lnu.se/research-groups/computational-chemistry-and-biochemistry-group?l=en From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of Olga Ivchenko [olga.ivche...@gmail.com] Sent: 02 December 2010 14:59 To: jalem...@vt.edu; Discussion list for GROMACS users Subject: Re: [gmx-users] proton proton transfer Thnaks, Justin. Probably CHARMM is suitable for this. 2010/12/2 Justin A. Lemkul jalem...@vt.edumailto:jalem...@vt.edu Olga Ivchenko wrote: Dear gromacs users, I want to simulate proton transfer between water and another small molecule in gromacs. In the end I should have the velosity of proton proton exchange. Please can you advice me which method is better to use for this in gromacs. I read about umbrella sampling, but may be there is other techniques? You can't do this with standard MD. Bonds cannot break and re-form in a classical force field. You might be able to do accomplish it with QM, however, but in that case you need to be looking outside of Gromacs. -Justin Yours sincerely, Olga -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.eduhttp://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.orgmailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.orgmailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] .pqr to .pdb
Dear Tsjerk some information exist in pdb file which are not peresent in pqr and vise versa. I want to convert them to eachother in a way to conclude one's information to the other file. as you know a typical pdb file has a definite colomns and each of them present a definite charachter(for example charge,X-coordinate,...) my pqr has more atoms than original pdb,but It dosen't have any coordinates. besides converting as you said dosen't solve the problem,because PYMOL can not read this converted file.it needs a file who has included atoms coordinates thanks in advance for your reply Mohsen On Thu, Nov 25, 2010 at 9:44 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hey, For this particular conversion you can also usually use 'mv': mv file.pqr file.pdb Btw, many of these file types are human readable. It usually helps quite a bit to look at the files and get acquainted with the file formats. Cheers, Tsjerk On Nov 22, 2010 12:42 PM, Mark Abraham mark.abra...@anu.edu.au wrote: On 22/11/2010 10:16 PM, mohsen ramezanpour wrote: Dear All I had a pdb file who was incompl... Ask it for a pdb format. There should be no tool that builds atoms that cannot write a standard file format like PDB - particularly as PQR is a derivative of PDB. Oh, and this is a bit off-topic for this list :-) 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/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] .pqr to .pdb
mohsen ramezanpour wrote: Dear Tsjerk some information exist in pdb file which are not peresent in pqr and vise versa. I want to convert them to eachother in a way to conclude one's information to the other file. as you know a typical pdb file has a definite colomns and each of them present a definite charachter(for example charge,X-coordinate,...) Charges are not typically in .pdb files, and they certainly don't precede the x-coordinate. my pqr has more atoms than original pdb,but It dosen't have any coordinates. Then it sounds like you have a useless .pqr file. The format of a proper .pqr file is identical to that of a .pdb file, except that in place of B-factor and occupancy fields, the charge and radius are given. Thus, what Tsjerk told you should work, but perhaps you have a mangled input file that makes this impossible. -Justin besides converting as you said dosen't solve the problem,because PYMOL can not read this converted file.it http://file.it needs a file who has included atoms coordinates thanks in advance for your reply Mohsen On Thu, Nov 25, 2010 at 9:44 PM, Tsjerk Wassenaar tsje...@gmail.com mailto:tsje...@gmail.com wrote: Hey, For this particular conversion you can also usually use 'mv': mv file.pqr file.pdb Btw, many of these file types are human readable. It usually helps quite a bit to look at the files and get acquainted with the file formats. Cheers, Tsjerk On Nov 22, 2010 12:42 PM, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote: On 22/11/2010 10:16 PM, mohsen ramezanpour wrote: Dear All I had a pdb file who was incompl... Ask it for a pdb format. There should be no tool that builds atoms that cannot write a standard file format like PDB - particularly as PQR is a derivative of PDB. Oh, and this is a bit off-topic for this list :-) Mark -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] .pqr to .pdb
Hi, if your pqr file has not coordinates, is impossible convert to PDB. What is the format of the original file?. However, the PQR file normally has more atoms because add hydrogens. Can you paste a little part of your pqr and pdb? Best regards Maxi On Thu, Dec 2, 2010 at 3:24 PM, mohsen ramezanpour ramezanpour.moh...@gmail.com wrote: Dear Tsjerk some information exist in pdb file which are not peresent in pqr and vise versa. I want to convert them to eachother in a way to conclude one's information to the other file. as you know a typical pdb file has a definite colomns and each of them present a definite charachter(for example charge,X-coordinate,...) my pqr has more atoms than original pdb,but It dosen't have any coordinates. besides converting as you said dosen't solve the problem,because PYMOL can not read this converted file.it needs a file who has included atoms coordinates thanks in advance for your reply Mohsen On Thu, Nov 25, 2010 at 9:44 PM, Tsjerk Wassenaar tsje...@gmail.comwrote: Hey, For this particular conversion you can also usually use 'mv': mv file.pqr file.pdb Btw, many of these file types are human readable. It usually helps quite a bit to look at the files and get acquainted with the file formats. Cheers, Tsjerk On Nov 22, 2010 12:42 PM, Mark Abraham mark.abra...@anu.edu.au wrote: On 22/11/2010 10:16 PM, mohsen ramezanpour wrote: Dear All I had a pdb file who was incompl... Ask it for a pdb format. There should be no tool that builds atoms that cannot write a standard file format like PDB - particularly as PQR is a derivative of PDB. Oh, and this is a bit off-topic for this list :-) 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/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] .pqr to .pdb
On Thu, Dec 2, 2010 at 5:58 PM, Justin A. Lemkul jalem...@vt.edu wrote: mohsen ramezanpour wrote: Dear Tsjerk some information exist in pdb file which are not peresent in pqr and vise versa. I want to convert them to eachother in a way to conclude one's information to the other file. as you know a typical pdb file has a definite colomns and each of them present a definite charachter(for example charge,X-coordinate,...) Charges are not typically in .pdb files, and they certainly don't precede the x-coordinate. Ok.I agree with you my pqr has more atoms than original pdb,but It dosen't have any coordinates. Then it sounds like you have a useless .pqr file. The format of a proper .pqr file is identical to that of a .pdb file, except that in place of B-factor and occupancy fields, the charge and radius are given. Thus, what Tsjerk told you should work, but perhaps you have a mangled input file that makes this impossible. Ok.I will try to produce another .pqr file again.I think both are you are right ,it seems to me my file is useless. Thanks -Justin besides converting as you said dosen't solve the problem,because PYMOL can not read this converted file.it http://file.it needs a file who has included atoms coordinates thanks in advance for your reply Mohsen On Thu, Nov 25, 2010 at 9:44 PM, Tsjerk Wassenaar tsje...@gmail.commailto: tsje...@gmail.com wrote: Hey, For this particular conversion you can also usually use 'mv': mv file.pqr file.pdb Btw, many of these file types are human readable. It usually helps quite a bit to look at the files and get acquainted with the file formats. Cheers, Tsjerk On Nov 22, 2010 12:42 PM, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote: On 22/11/2010 10:16 PM, mohsen ramezanpour wrote: Dear All I had a pdb file who was incompl... Ask it for a pdb format. There should be no tool that builds atoms that cannot write a standard file format like PDB - particularly as PQR is a derivative of PDB. Oh, and this is a bit off-topic for this list :-) Mark -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: individual lateral diffusion coefficients
Hi Javier I think I saw this in several mails of this list and it is also implicit in the Justin tutorial for analysis of bilayers. I am not sure whether or not this has also been published... I do not remember any paper. I think this is reasonable for lipids in contact with membrane proteins because only a part of the lipid could be tied to the protein... then the diffusion for different parts of the lipid could be different. I think I will calculate the diffusion for each lipid individually... If you are interested in comparing results you could contact me off the list. Saludos, Ángel. On Thu, 2010-12-02 at 14:22 +0100, Javier Cerezo wrote: Hi Ángel Can you provide a citation about the use of only PO4 atoms to calculate the diffusion constant? Is it always recommended or just with CG simulations? I'm also working on diffusion calculation and that will be interesting. By the way, regarding the index files I mentioned, it might be better to have a group of lipids that are at a certain distance from the protein in the same index, again to improve sampling (maybe this is not a way to improve sampling, I don't know). Thanks Javier El 02/12/10 13:56, Ángel Piñeiro escribió: Hi Javier 1.- you are right! the diff_mol.xvg file I reported was from a previous attempt in which I used the whole lipid molecules with the -mol option on, instead of the PO4 beads with -mol off. Sorry for this confusion 2.- As I said above, I did attempts using both the whole molecule and the PO4 beads. Yes I saw the figure 6 in the Wolhert Edholm's paper but I read in several other references that the calculation is more accurate by using only the P atom... what makes sense to me mainly for the lipids which are in contact with proteins 3.- I agree that removing jumps does not change anything. I decided to give this information in my message to avoid a reply saying try to remove jumps ;) 4.- Yes I agree that I could do the calculation by creating an index for each lipid... I guess that is the safest way to proceed... Thanks for your reply! Ángel. On Thu, 2010-12-02 at 13:30 +0100, Javier Cerezo wrote: Hello Ángel. Well, there are a some things that I don't understand about your calculation, but might be just a problem of mine. Here you have my comments: 1. How do you get the diff_mol.xvg file if you are not using -mol in your command line input (and you index file has broken molecules). 2. Why do you select just an atom to calculate the diffusion? According to Wolhert and Edholm (JCP, 125, 204703) the MSD for all lipids atoms reach the same slope, so I guess using them all could improve sampling (I'm not sure). 3. I think that reprocessing of your trajectory to remove jumps is no longer needed (I got the same results in a recent test using version 4.5.1). 4. What I would do to calculate D as funtion to the distance to the membrane protein is generate different index files containing lipids according to this distance (and hoping they don't move a lot during the simulation) and run different msd calculations. I think I have read in the mailing list about a script to make such a selection regarding distances to construct the index file or just make your own one. Good luck Javier El 02/12/10 12:50, Ángel Piñeiro escribió: I want to add that the MSD as a function of time (msd.xvg file) looks completely linear Greetings, Ángel Piñeiro. On Thu, 2010-12-02 at 12:45 +0100, Ángel Piñeiro wrote: Dear all, I aim to calculate the lateral diffusion coefficients of lipids as a function of the distance to a membrane protein using the Martini force field. For this I guess I could use the diff_mol.xvg output file of the g_msd command which provides the list of diffusion coefficients for each lipid (I guess the lipids are ordered as in the trajectory file). Then I would calculate the protein-lipid distance for each lipid and I would generate the diffusion vs distance file. Before starting the calculations on the membrane protein system I tested the g_msd command on a DPPC bilayer. In my bilayer simulation I removed the COM of lipids and water separately. Before analyzing it I removed jumps over the box boundaries using trjconv -pbc nojump and I created a index file with the PO4 atoms as a new group. Then I executed the following command: g_msd -s topol.tpr -f trajnojump.xtc -n p.ndx -lateral z -rmcomm from which I get the following output: D[ PO4] 0.0958 (+/- 0.0135) 1e-5 cm^2/s I think the value is not crazy for DPPC at 323 K using Martini... but I noticed that the D values for the independent lipids reported in the diff_mol.xvg file range from 0.0021959 to 0.482909
Re: [gmx-users] Re: individual lateral diffusion coefficients
Ángel Piñeiro wrote: Hi Javier I think I saw this in several mails of this list and it is also implicit in the Justin tutorial for analysis of bilayers. I am not sure whether or not this has also been published... I do not remember any paper. I think this is reasonable for lipids in contact with membrane proteins because only a part of the lipid could be tied to the protein... then the diffusion for different parts of the lipid could be different. I think I will calculate the diffusion for each lipid individually... If you are interested in comparing results you could contact me off the list. I haven't followed this thread at all, but I saw my name come up :) This is what I have always based my g_msd calculations on: http://lists.gromacs.org/pipermail/gmx-users/2008-January/031804.html -Justin Saludos, Ángel. On Thu, 2010-12-02 at 14:22 +0100, Javier Cerezo wrote: Hi Ángel Can you provide a citation about the use of only PO4 atoms to calculate the diffusion constant? Is it always recommended or just with CG simulations? I'm also working on diffusion calculation and that will be interesting. By the way, regarding the index files I mentioned, it might be better to have a group of lipids that are at a certain distance from the protein in the same index, again to improve sampling (maybe this is not a way to improve sampling, I don't know). Thanks Javier El 02/12/10 13:56, Ángel Piñeiro escribió: Hi Javier 1.- you are right! the diff_mol.xvg file I reported was from a previous attempt in which I used the whole lipid molecules with the -mol option on, instead of the PO4 beads with -mol off. Sorry for this confusion 2.- As I said above, I did attempts using both the whole molecule and the PO4 beads. Yes I saw the figure 6 in the Wolhert Edholm's paper but I read in several other references that the calculation is more accurate by using only the P atom... what makes sense to me mainly for the lipids which are in contact with proteins 3.- I agree that removing jumps does not change anything. I decided to give this information in my message to avoid a reply saying try to remove jumps ;) 4.- Yes I agree that I could do the calculation by creating an index for each lipid... I guess that is the safest way to proceed... Thanks for your reply! Ángel. On Thu, 2010-12-02 at 13:30 +0100, Javier Cerezo wrote: Hello Ángel. Well, there are a some things that I don't understand about your calculation, but might be just a problem of mine. Here you have my comments: 1. How do you get the diff_mol.xvg file if you are not using -mol in your command line input (and you index file has broken molecules). 2. Why do you select just an atom to calculate the diffusion? According to Wolhert and Edholm (JCP, 125, 204703) the MSD for all lipids atoms reach the same slope, so I guess using them all could improve sampling (I'm not sure). 3. I think that reprocessing of your trajectory to remove jumps is no longer needed (I got the same results in a recent test using version 4.5.1). 4. What I would do to calculate D as funtion to the distance to the membrane protein is generate different index files containing lipids according to this distance (and hoping they don't move a lot during the simulation) and run different msd calculations. I think I have read in the mailing list about a script to make such a selection regarding distances to construct the index file or just make your own one. Good luck Javier El 02/12/10 12:50, Ángel Piñeiro escribió: I want to add that the MSD as a function of time (msd.xvg file) looks completely linear Greetings, Ángel Piñeiro. On Thu, 2010-12-02 at 12:45 +0100, Ángel Piñeiro wrote: Dear all, I aim to calculate the lateral diffusion coefficients of lipids as a function of the distance to a membrane protein using the Martini force field. For this I guess I could use the diff_mol.xvg output file of the g_msd command which provides the list of diffusion coefficients for each lipid (I guess the lipids are ordered as in the trajectory file). Then I would calculate the protein-lipid distance for each lipid and I would generate the diffusion vs distance file. Before starting the calculations on the membrane protein system I tested the g_msd command on a DPPC bilayer. In my bilayer simulation I removed the COM of lipids and water separately. Before analyzing it I removed jumps over the box boundaries using trjconv -pbc nojump and I created a index file with the PO4 atoms as a new group. Then I executed the following command: g_msd -s topol.tpr -f trajnojump.xtc -n p.ndx -lateral z -rmcomm from which I get the following output: D[ PO4] 0.0958 (+/- 0.0135) 1e-5 cm^2/s I think the value is not crazy for DPPC at 323 K using Martini... but I noticed that the D values for the independent lipids reported in the diff_mol.xvg file range from 0.0021959 to 0.482909 cm^2/s. If the differences are so high
Re: [gmx-users] proton proton transfer
Olga Ivchenko skrev 2010-12-02 13.30: Dear gromacs users, I want to simulate proton transfer between water and another small molecule in gromacs. In the end I should have the velosity of proton proton exchange. Please can you advice me which method is better to use for this in gromacs. I read about umbrella sampling, but may be there is other techniques? Yours sincerely, Olga I am working on a protocol to include proton transfer in classical gromacs simulations. Unfortunately it will note be ready for at least a month, so if you're in a hurry you'll have to do it with e.g. QM/MM. Erik -- --- Erik Marklund, PhD student Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 4537fax: +46 18 511 755 er...@xray.bmc.uu.sehttp://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/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: individual lateral diffusion coefficients
Thanks Justin. Do you the reason behind? I am trying following that protocol and my P curve in not as linear as All-lipid-atoms one (DPPC, FF: G53a6, t=50ns). Furthermore, regarding the linear region, the slopes are not the same. So which one do you think is more accurate? Thanks again Javier El 02/12/10 16:09, Justin A. Lemkul escribió: Ángel Piñeiro wrote: Hi Javier I think I saw this in several mails of this list and it is also implicit in the Justin tutorial for analysis of bilayers. I am not sure whether or not this has also been published... I do not remember any paper. I think this is reasonable for lipids in contact with membrane proteins because only a part of the lipid could be tied to the protein... then the diffusion for different parts of the lipid could be different. I think I will calculate the diffusion for each lipid individually... If you are interested in comparing results you could contact me off the list. I haven't followed this thread at all, but I saw my name come up :) This is what I have always based my g_msd calculations on: http://lists.gromacs.org/pipermail/gmx-users/2008-January/031804.html -Justin Saludos, Ángel. On Thu, 2010-12-02 at 14:22 +0100, Javier Cerezo wrote: Hi Ángel Can you provide a citation about the use of only PO4 atoms to calculate the diffusion constant? Is it always recommended or just with CG simulations? I'm also working on diffusion calculation and that will be interesting. By the way, regarding the index files I mentioned, it might be better to have a group of lipids that are at a certain distance from the protein in the same index, again to improve sampling (maybe this is not a way to improve sampling, I don't know). Thanks Javier El 02/12/10 13:56, Ángel Piñeiro escribió: Hi Javier 1.- you are right! the diff_mol.xvg file I reported was from a previous attempt in which I used the whole lipid molecules with the -mol option on, instead of the PO4 beads with -mol off. Sorry for this confusion 2.- As I said above, I did attempts using both the whole molecule and the PO4 beads. Yes I saw the figure 6 in the Wolhert Edholm's paper but I read in several other references that the calculation is more accurate by using only the P atom... what makes sense to me mainly for the lipids which are in contact with proteins 3.- I agree that removing jumps does not change anything. I decided to give this information in my message to avoid a reply saying try to remove jumps ;) 4.- Yes I agree that I could do the calculation by creating an index for each lipid... I guess that is the safest way to proceed... Thanks for your reply! Ángel. On Thu, 2010-12-02 at 13:30 +0100, Javier Cerezo wrote: Hello Ángel. Well, there are a some things that I don't understand about your calculation, but might be just a problem of mine. Here you have my comments: 1. How do you get the diff_mol.xvg file if you are not using -mol in your command line input (and you index file has broken molecules). 2. Why do you select just an atom to calculate the diffusion? According to Wolhert and Edholm (JCP, 125, 204703) the MSD for all lipids atoms reach the same slope, so I guess using them all could improve sampling (I'm not sure). 3. I think that reprocessing of your trajectory to remove jumps is no longer needed (I got the same results in a recent test using version 4.5.1). 4. What I would do to calculate D as funtion to the distance to the membrane protein is generate different index files containing lipids according to this distance (and hoping they don't move a lot during the simulation) and run different msd calculations. I think I have read in the mailing list about a script to make such a selection regarding distances to construct the index file or just make your own one. Good luck Javier El 02/12/10 12:50, Ángel Piñeiro escribió: I want to add that the MSD as a function of time (msd.xvg file) looks completely linear Greetings, Ángel Piñeiro. On Thu, 2010-12-02 at 12:45 +0100, Ángel Piñeiro wrote: Dear all, I aim to calculate the lateral diffusion coefficients of lipids as a function of the distance to a membrane protein using the Martini force field. For this I guess I could use the diff_mol.xvg output file of the g_msd command which provides the list of diffusion coefficients for each lipid (I guess the lipids are ordered as in the trajectory file). Then I would calculate the protein-lipid distance for each lipid and I would generate the diffusion vs distance file. Before starting the calculations on the membrane protein system I tested the g_msd command on a DPPC bilayer. In my bilayer simulation I removed the COM of lipids and water separately. Before analyzing it I removed jumps over the box boundaries using trjconv -pbc nojump and I created a index file with the PO4 atoms as a new group. Then I executed the following command: g_msd -s topol.tpr -f trajnojump.xtc -n
Re: [gmx-users] Re: individual lateral diffusion coefficients
Sorry for the misspell... Thanks Justin. Do you *know* the reason behind? I am trying following that protocol and my P curve in not as linear as All-lipid-atoms one (DPPC, FF: G53a6, t=50ns). Furthermore, regarding the linear region, the slopes are not the same. So which one do you think is more accurate? Thanks again Javier El 02/12/10 16:09, Justin A. Lemkul escribió: Ángel Piñeiro wrote: Hi Javier I think I saw this in several mails of this list and it is also implicit in the Justin tutorial for analysis of bilayers. I am not sure whether or not this has also been published... I do not remember any paper. I think this is reasonable for lipids in contact with membrane proteins because only a part of the lipid could be tied to the protein... then the diffusion for different parts of the lipid could be different. I think I will calculate the diffusion for each lipid individually... If you are interested in comparing results you could contact me off the list. I haven't followed this thread at all, but I saw my name come up :) This is what I have always based my g_msd calculations on: http://lists.gromacs.org/pipermail/gmx-users/2008-January/031804.html -Justin Saludos, Ángel. On Thu, 2010-12-02 at 14:22 +0100, Javier Cerezo wrote: Hi Ángel Can you provide a citation about the use of only PO4 atoms to calculate the diffusion constant? Is it always recommended or just with CG simulations? I'm also working on diffusion calculation and that will be interesting. By the way, regarding the index files I mentioned, it might be better to have a group of lipids that are at a certain distance from the protein in the same index, again to improve sampling (maybe this is not a way to improve sampling, I don't know). Thanks Javier El 02/12/10 13:56, Ángel Piñeiro escribió: Hi Javier 1.- you are right! the diff_mol.xvg file I reported was from a previous attempt in which I used the whole lipid molecules with the -mol option on, instead of the PO4 beads with -mol off. Sorry for this confusion 2.- As I said above, I did attempts using both the whole molecule and the PO4 beads. Yes I saw the figure 6 in the Wolhert Edholm's paper but I read in several other references that the calculation is more accurate by using only the P atom... what makes sense to me mainly for the lipids which are in contact with proteins 3.- I agree that removing jumps does not change anything. I decided to give this information in my message to avoid a reply saying try to remove jumps ;) 4.- Yes I agree that I could do the calculation by creating an index for each lipid... I guess that is the safest way to proceed... Thanks for your reply! Ángel. On Thu, 2010-12-02 at 13:30 +0100, Javier Cerezo wrote: Hello Ángel. Well, there are a some things that I don't understand about your calculation, but might be just a problem of mine. Here you have my comments: 1. How do you get the diff_mol.xvg file if you are not using -mol in your command line input (and you index file has broken molecules). 2. Why do you select just an atom to calculate the diffusion? According to Wolhert and Edholm (JCP, 125, 204703) the MSD for all lipids atoms reach the same slope, so I guess using them all could improve sampling (I'm not sure). 3. I think that reprocessing of your trajectory to remove jumps is no longer needed (I got the same results in a recent test using version 4.5.1). 4. What I would do to calculate D as funtion to the distance to the membrane protein is generate different index files containing lipids according to this distance (and hoping they don't move a lot during the simulation) and run different msd calculations. I think I have read in the mailing list about a script to make such a selection regarding distances to construct the index file or just make your own one. Good luck Javier El 02/12/10 12:50, Ángel Piñeiro escribió: I want to add that the MSD as a function of time (msd.xvg file) looks completely linear Greetings, Ángel Piñeiro. On Thu, 2010-12-02 at 12:45 +0100, Ángel Piñeiro wrote: Dear all, I aim to calculate the lateral diffusion coefficients of lipids as a function of the distance to a membrane protein using the Martini force field. For this I guess I could use the diff_mol.xvg output file of the g_msd command which provides the list of diffusion coefficients for each lipid (I guess the lipids are ordered as in the trajectory file). Then I would calculate the protein-lipid distance for each lipid and I would generate the diffusion vs distance file. Before starting the calculations on the membrane protein system I tested the g_msd command on a DPPC bilayer. In my bilayer simulation I removed the COM of lipids and water separately. Before analyzing it I removed jumps over the box boundaries using trjconv -pbc nojump and I created a index file with the PO4 atoms as a new group. Then I executed the following command: g_msd
Re: [gmx-users] .pqr to .pdb
Dear Maximiliano I reproduce my .pqr file and it has coordinate files too. I performed what Tsjerk said and I could convert pqr tp pdb file successfully Thanks for all Mohsen On Thu, Dec 2, 2010 at 6:00 PM, Maximiliano Figueroa maxfi...@gmail.comwrote: Hi, if your pqr file has not coordinates, is impossible convert to PDB. What is the format of the original file?. However, the PQR file normally has more atoms because add hydrogens. Can you paste a little part of your pqr and pdb? Best regards Maxi On Thu, Dec 2, 2010 at 3:24 PM, mohsen ramezanpour ramezanpour.moh...@gmail.com wrote: Dear Tsjerk some information exist in pdb file which are not peresent in pqr and vise versa. I want to convert them to eachother in a way to conclude one's information to the other file. as you know a typical pdb file has a definite colomns and each of them present a definite charachter(for example charge,X-coordinate,...) my pqr has more atoms than original pdb,but It dosen't have any coordinates. besides converting as you said dosen't solve the problem,because PYMOL can not read this converted file.it needs a file who has included atoms coordinates thanks in advance for your reply Mohsen On Thu, Nov 25, 2010 at 9:44 PM, Tsjerk Wassenaar tsje...@gmail.comwrote: Hey, For this particular conversion you can also usually use 'mv': mv file.pqr file.pdb Btw, many of these file types are human readable. It usually helps quite a bit to look at the files and get acquainted with the file formats. Cheers, Tsjerk On Nov 22, 2010 12:42 PM, Mark Abraham mark.abra...@anu.edu.au wrote: On 22/11/2010 10:16 PM, mohsen ramezanpour wrote: Dear All I had a pdb file who was incompl... Ask it for a pdb format. There should be no tool that builds atoms that cannot write a standard file format like PDB - particularly as PQR is a derivative of PDB. Oh, and this is a bit off-topic for this list :-) 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/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Note on oscillation period / time step
GMX Users: When I run grompp on methanol in water in v. 4.5.3 I get the following Note: NOTE 1 [file methanol.top, line 73]: The bond in molecule-type MET between atoms 5 OA and 6 HO has an estimated oscillational period of 9.0e-03 ps, which is less than 10 times the time step of 1.0e-03 ps. Maybe you forgot to change the constraints mdp option. Here is my mdp file: ; User Robin ; Wed Dec.1 2010 ; Input file ; title = Yo cpp = /lib/cpp integrator = md dt = 0.001; ps ! nsteps = 110 ; total 1000 ps=1 ns nstcomm = 10 ; (x) coordinates, (v) is velocities, (f) is forces ; This affects traj.trr ; these numbers shouldn't be too small (100,000), takes up disk space nstxout = 1000 nstvout = 1000 nstfout = 1000 ; Output frequency for energies nstlog = 100 nstenergy = 100 ; This affects .xtc file for movies this should be a fairly small number nstxtcout = 100 xtc-precision = 1000 ; parameters for neighbors nstlist = 10 ns_type = grid rlist = 0.9 ; electrostatics coulombtype = pme pme_order = 4 ewald_rtol = 1e-5 ewald_geometry = 3d epsilon_surface = 0 fourierspacing = 0.1 fourier_nx = 0.0 fourier_ny = 0.0 fourier_nz = 0.0 rcoulomb= 0.9 optimize_fft= yes Dispcorr= EnerPres vdwtype = cutoff rvdw_switch = 0.85 rvdw= 0.9 ; Berendsen temperature coupling is on in two groups Tcoupl = v_rescale tc-grps = system tau_t = 0.1 ref_t = 300 ; Energy monitoring energygrps = MET SOL ; Isotropic pressure coupling is now on Pcoupl = berendsen Pcoupltype = isotropic tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is off at 300 K. gen_vel = no gen_temp= 300.0 gen_seed= 173529 Here is my top file: ; ; ; Include forcefield parameters #include ffoplsaa.itp ; ; Methanol, Jorgensen et al. JACS 118 pp. 11225 (1996) ; [ moleculetype ] ; name nrexcl MET 3 [ atoms ] ; nrtype resnr residuatomcgnrcharge mass 1 opls_157 1 METC 1 0.145 2 opls_156 1 METH 1 0.04 3 opls_156 1 METH 1 0.04 4 opls_156 1 METH 1 0.04 5 opls_154 1 MET OA 1 -0.683 6 opls_155 1 MET HO 1 0.418 [ bonds ] ; aiaj funct c0 c1 1 2 1 1 3 1 1 4 1 1 5 1 5 6 1 [ pairs ] ; i j funct 2 6 3 6 4 6 [ angles ] ; aiajak funct c0c1 ; H3 2 1 5 1 3 1 5 1 4 1 5 1 4 1 3 1 4 1 2 1 [ system ] ; Name MET in water [ molecules ] ; Compound#mols MET 1 SOL 503 Do I need to add some sort of constraint on my methanol molecule? Thanks, Robin -- Robin C. Underwood Chemistry Department 560 Oval Drive West Lafayette, IN 47907 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Note on oscillation period / time step
Hello. It looks like you're missing the bonded-interactions parameters. [ bonds ] ; aiaj funct*R0 Kb *1 2 1* XX* 1 3 1* XX* 1 4 1* XX* 1 5 1* XX* 5 6 1* XX* (also angles...) Is it implicit somewhere? I don't know if it is automatic and if so, from where the parameters are taken. If it is by using atoms names and the ffbonded.itp from oplsaa, then atom name OA is missing in the itp file. I think that, according to the code (grompp.c), this note may arise if the force constants are zero. Javier El 02/12/10 17:11, Robin C. Underwood escribió: GMX Users: When I run grompp on methanol in water in v. 4.5.3 I get the following Note: NOTE 1 [file methanol.top, line 73]: The bond in molecule-type MET between atoms 5 OA and 6 HO has an estimated oscillational period of 9.0e-03 ps, which is less than 10 times the time step of 1.0e-03 ps. Maybe you forgot to change the constraints mdp option. Here is my mdp file: ; User Robin ; Wed Dec.1 2010 ; Input file ; title = Yo cpp = /lib/cpp integrator = md dt = 0.001; ps ! nsteps = 110 ; total 1000 ps=1 ns nstcomm = 10 ; (x) coordinates, (v) is velocities, (f) is forces ; This affects traj.trr ; these numbers shouldn't be too small (100,000), takes up disk space nstxout = 1000 nstvout = 1000 nstfout = 1000 ; Output frequency for energies nstlog = 100 nstenergy = 100 ; This affects .xtc file for movies this should be a fairly small number nstxtcout = 100 xtc-precision = 1000 ; parameters for neighbors nstlist = 10 ns_type = grid rlist = 0.9 ; electrostatics coulombtype = pme pme_order = 4 ewald_rtol = 1e-5 ewald_geometry = 3d epsilon_surface = 0 fourierspacing = 0.1 fourier_nx = 0.0 fourier_ny = 0.0 fourier_nz = 0.0 rcoulomb= 0.9 optimize_fft= yes Dispcorr= EnerPres vdwtype = cutoff rvdw_switch = 0.85 rvdw= 0.9 ; Berendsen temperature coupling is on in two groups Tcoupl = v_rescale tc-grps = system tau_t = 0.1 ref_t = 300 ; Energy monitoring energygrps = MET SOL ; Isotropic pressure coupling is now on Pcoupl = berendsen Pcoupltype = isotropic tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is off at 300 K. gen_vel = no gen_temp= 300.0 gen_seed= 173529 Here is my top file: ; ; ; Include forcefield parameters #include ffoplsaa.itp ; ; Methanol, Jorgensen et al. JACS 118 pp. 11225 (1996) ; [ moleculetype ] ; name nrexcl MET 3 [ atoms ] ; nrtype resnr residuatomcgnrcharge mass 1 opls_157 1 METC 1 0.145 2 opls_156 1 METH 1 0.04 3 opls_156 1 METH 1 0.04 4 opls_156 1 METH 1 0.04 5 opls_154 1 MET OA 1 -0.683 6 opls_155 1 MET HO 1 0.418 [ bonds ] ; aiaj funct c0 c1 1 2 1 1 3 1 1 4 1 1 5 1 5 6 1 [ pairs ] ; i j funct 2 6 3 6 4 6 [ angles ] ; aiajak funct c0c1 ; H3 2 1 5 1 3 1 5 1 4 1 5 1 4 1 3 1 4 1 2 1 [ system ] ; Name MET in water [ molecules ] ; Compound#mols MET 1 SOL 503 Do I need to add some sort of constraint on my methanol molecule? Thanks, Robin -- Javier CEREZO BASTIDA Estudiante de Doctorado - Dpto. Química-Física Universidad de Murcia 30100 MURCIA (España) Tlf.(+34)868887434 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Note on oscillation period / time step
Robin, Easiest way to get it running, with the flexible bond between O and H in methane would be to decrease the time step. I would start with half a femto second time step and see what happens. All the best Rajesh On Thu, Dec 2, 2010 at 10:11 AM, Robin C. Underwood rcund...@purdue.eduwrote: GMX Users: When I run grompp on methanol in water in v. 4.5.3 I get the following Note: NOTE 1 [file methanol.top, line 73]: The bond in molecule-type MET between atoms 5 OA and 6 HO has an estimated oscillational period of 9.0e-03 ps, which is less than 10 times the time step of 1.0e-03 ps. Maybe you forgot to change the constraints mdp option. Here is my mdp file: ; User Robin ; Wed Dec.1 2010 ; Input file ; title = Yo cpp = /lib/cpp integrator = md dt = 0.001; ps ! nsteps = 110 ; total 1000 ps=1 ns nstcomm = 10 ; (x) coordinates, (v) is velocities, (f) is forces ; This affects traj.trr ; these numbers shouldn't be too small (100,000), takes up disk space nstxout = 1000 nstvout = 1000 nstfout = 1000 ; Output frequency for energies nstlog = 100 nstenergy = 100 ; This affects .xtc file for movies this should be a fairly small number nstxtcout = 100 xtc-precision = 1000 ; parameters for neighbors nstlist = 10 ns_type = grid rlist = 0.9 ; electrostatics coulombtype = pme pme_order = 4 ewald_rtol = 1e-5 ewald_geometry = 3d epsilon_surface = 0 fourierspacing = 0.1 fourier_nx = 0.0 fourier_ny = 0.0 fourier_nz = 0.0 rcoulomb= 0.9 optimize_fft= yes Dispcorr= EnerPres vdwtype = cutoff rvdw_switch = 0.85 rvdw= 0.9 ; Berendsen temperature coupling is on in two groups Tcoupl = v_rescale tc-grps = system tau_t = 0.1 ref_t = 300 ; Energy monitoring energygrps = MET SOL ; Isotropic pressure coupling is now on Pcoupl = berendsen Pcoupltype = isotropic tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is off at 300 K. gen_vel = no gen_temp= 300.0 gen_seed= 173529 Here is my top file: ; ; ; Include forcefield parameters #include ffoplsaa.itp ; ; Methanol, Jorgensen et al. JACS 118 pp. 11225 (1996) ; [ moleculetype ] ; name nrexcl MET 3 [ atoms ] ; nrtype resnr residuatomcgnrcharge mass 1 opls_157 1 METC 1 0.145 2 opls_156 1 METH 1 0.04 3 opls_156 1 METH 1 0.04 4 opls_156 1 METH 1 0.04 5 opls_154 1 MET OA 1 -0.683 6 opls_155 1 MET HO 1 0.418 [ bonds ] ; aiaj funct c0 c1 1 2 1 1 3 1 1 4 1 1 5 1 5 6 1 [ pairs ] ; i j funct 2 6 3 6 4 6 [ angles ] ; aiajak funct c0c1 ; H3 2 1 5 1 3 1 5 1 4 1 5 1 4 1 3 1 4 1 2 1 [ system ] ; Name MET in water [ molecules ] ; Compound#mols MET 1 SOL 503 Do I need to add some sort of constraint on my methanol molecule? Thanks, Robin -- Robin C. Underwood Chemistry Department 560 Oval Drive West Lafayette, IN 47907 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Naga Rajesh Tummala, PhD School of Chemical, Biological, and Materials Engineering University of Oklahoma -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Note on oscillation period / time step
Javier Cerezo wrote: Hello. It looks like you're missing the bonded-interactions parameters. [ bonds ] ; aiaj funct *R0 Kb *1 2 1 * XX* 1 3 1 * XX* 1 4 1 * XX* 1 5 1 * XX* 5 6 1 * XX* (also angles...) Is it implicit somewhere? I don't know if it is automatic and if so, from where the parameters are taken. If it is by using atoms names and the ffbonded.itp from oplsaa, then atom name OA is missing in the itp file. I think that, according to the code (grompp.c), this note may arise if the force constants are zero. Atom types are interpolated from ffbonded.itp and assigned. If the problem were in the bonded parameters, a very different fatal error arises. There is no problem here. -Justin Javier El 02/12/10 17:11, Robin C. Underwood escribió: GMX Users: When I run grompp on methanol in water in v. 4.5.3 I get the following Note: NOTE 1 [file methanol.top, line 73]: The bond in molecule-type MET between atoms 5 OA and 6 HO has an estimated oscillational period of 9.0e-03 ps, which is less than 10 times the time step of 1.0e-03 ps. Maybe you forgot to change the constraints mdp option. Here is my mdp file: ; User Robin ; Wed Dec.1 2010 ; Input file ; title = Yo cpp = /lib/cpp integrator = md dt = 0.001; ps ! nsteps = 110 ; total 1000 ps=1 ns nstcomm = 10 ; (x) coordinates, (v) is velocities, (f) is forces ; This affects traj.trr ; these numbers shouldn't be too small (100,000), takes up disk space nstxout = 1000 nstvout = 1000 nstfout = 1000 ; Output frequency for energies nstlog = 100 nstenergy = 100 ; This affects .xtc file for movies this should be a fairly small number nstxtcout = 100 xtc-precision = 1000 ; parameters for neighbors nstlist = 10 ns_type = grid rlist = 0.9 ; electrostatics coulombtype = pme pme_order = 4 ewald_rtol = 1e-5 ewald_geometry = 3d epsilon_surface = 0 fourierspacing = 0.1 fourier_nx = 0.0 fourier_ny = 0.0 fourier_nz = 0.0 rcoulomb= 0.9 optimize_fft= yes Dispcorr= EnerPres vdwtype = cutoff rvdw_switch = 0.85 rvdw= 0.9 ; Berendsen temperature coupling is on in two groups Tcoupl = v_rescale tc-grps = system tau_t = 0.1 ref_t = 300 ; Energy monitoring energygrps = MET SOL ; Isotropic pressure coupling is now on Pcoupl = berendsen Pcoupltype = isotropic tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is off at 300 K. gen_vel = no gen_temp= 300.0 gen_seed= 173529 Here is my top file: ; ; ; Include forcefield parameters #include ffoplsaa.itp ; ; Methanol, Jorgensen et al. JACS 118 pp. 11225 (1996) ; [ moleculetype ] ; name nrexcl MET 3 [ atoms ] ; nrtype resnr residuatomcgnrcharge mass 1 opls_157 1 METC 1 0.145 2 opls_156 1 METH 1 0.04 3 opls_156 1 METH 1 0.04 4 opls_156 1 METH 1 0.04 5 opls_154 1 MET OA 1 -0.683 6 opls_155 1 MET HO 1 0.418 [ bonds ] ; aiaj funct c0 c1 1 2 1 1 3 1 1 4 1 1 5 1 5 6 1 [ pairs ] ; i j funct 2 6 3 6 4 6 [ angles ] ; aiajak funct c0c1 ; H3 2 1 5 1 3 1 5 1 4 1 5 1 4 1 3 1 4 1 2 1 [ system ] ; Name MET in water [ molecules ] ; Compound#mols MET 1 SOL 503 Do I need to add some sort of constraint on my methanol molecule? Thanks, Robin -- Javier CEREZO BASTIDA Estudiante de Doctorado - Dpto. Química-Física Universidad de Murcia 30100 MURCIA (España) Tlf.(+34)868887434 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before
Re: [gmx-users] individual lateral diffusion coefficients
Ángel Piñeiro wrote: Dear all, I aim to calculate the lateral diffusion coefficients of lipids as a function of the distance to a membrane protein using the Martini force field. For this I guess I could use the diff_mol.xvg output file of the g_msd command which provides the list of diffusion coefficients for each lipid (I guess the lipids are ordered as in the trajectory file). Then I would calculate the protein-lipid distance for each lipid and I would generate the diffusion vs distance file. Before starting the calculations on the membrane protein system I tested the g_msd command on a DPPC bilayer. In my bilayer simulation I removed the COM of lipids and water separately. Before analyzing it I removed jumps over the box boundaries using trjconv -pbc nojump and I created a index file with the PO4 atoms as a new group. Then I executed the following command: g_msd -s topol.tpr -f trajnojump.xtc -n p.ndx -lateral z -rmcomm from which I get the following output: D[ PO4] 0.0958 (+/- 0.0135) 1e-5 cm^2/s I think the value is not crazy for DPPC at 323 K using Martini... but I noticed that the D values for the independent lipids reported in the diff_mol.xvg file range from 0.0021959 to 0.482909 cm^2/s. If the differences are so high for a single lipid bilayer I suspect that I will not observe significant differences as a function of the distance to the protein in my simulations of the whole system... probably I am doing something wrong¿? In my experience, this is to be expected. To calculate reliable diffusion coefficients, you need very well-converged data, and for individual lipids, this effect is even more pronounced. How long is your trajectory, and how often did you save snapshots? Note too, that the results of g_msd can be impacted by -trestart, -beginfit, -endfit, etc. -Justin Thanks for any advice Ángel Piñeiro. -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: individual lateral diffusion coefficients
Javier Cerezo wrote: Thanks Justin. Do you the reason behind? I am trying following that protocol and my P curve in not as linear as All-lipid-atoms one (DPPC, FF: G53a6, t=50ns). Furthermore, regarding the linear region, the slopes are not the same. So which one do you think is more accurate? I don't know. 50 ns is somewhat short, I think. You might have better luck with longer trajectories (100 ns). In principle (and in a perfect world), all force fields would agree, but in reality, this is not the case. Some models may simply perform better than others. -Justin Thanks again Javier El 02/12/10 16:09, Justin A. Lemkul escribió: Ángel Piñeiro wrote: Hi Javier I think I saw this in several mails of this list and it is also implicit in the Justin tutorial for analysis of bilayers. I am not sure whether or not this has also been published... I do not remember any paper. I think this is reasonable for lipids in contact with membrane proteins because only a part of the lipid could be tied to the protein... then the diffusion for different parts of the lipid could be different. I think I will calculate the diffusion for each lipid individually... If you are interested in comparing results you could contact me off the list. I haven't followed this thread at all, but I saw my name come up :) This is what I have always based my g_msd calculations on: http://lists.gromacs.org/pipermail/gmx-users/2008-January/031804.html -Justin Saludos, Ángel. On Thu, 2010-12-02 at 14:22 +0100, Javier Cerezo wrote: Hi Ángel Can you provide a citation about the use of only PO4 atoms to calculate the diffusion constant? Is it always recommended or just with CG simulations? I'm also working on diffusion calculation and that will be interesting. By the way, regarding the index files I mentioned, it might be better to have a group of lipids that are at a certain distance from the protein in the same index, again to improve sampling (maybe this is not a way to improve sampling, I don't know). Thanks Javier El 02/12/10 13:56, Ángel Piñeiro escribió: Hi Javier 1.- you are right! the diff_mol.xvg file I reported was from a previous attempt in which I used the whole lipid molecules with the -mol option on, instead of the PO4 beads with -mol off. Sorry for this confusion 2.- As I said above, I did attempts using both the whole molecule and the PO4 beads. Yes I saw the figure 6 in the Wolhert Edholm's paper but I read in several other references that the calculation is more accurate by using only the P atom... what makes sense to me mainly for the lipids which are in contact with proteins 3.- I agree that removing jumps does not change anything. I decided to give this information in my message to avoid a reply saying try to remove jumps ;) 4.- Yes I agree that I could do the calculation by creating an index for each lipid... I guess that is the safest way to proceed... Thanks for your reply! Ángel. On Thu, 2010-12-02 at 13:30 +0100, Javier Cerezo wrote: Hello Ángel. Well, there are a some things that I don't understand about your calculation, but might be just a problem of mine. Here you have my comments: 1. How do you get the diff_mol.xvg file if you are not using -mol in your command line input (and you index file has broken molecules). 2. Why do you select just an atom to calculate the diffusion? According to Wolhert and Edholm (JCP, 125, 204703) the MSD for all lipids atoms reach the same slope, so I guess using them all could improve sampling (I'm not sure). 3. I think that reprocessing of your trajectory to remove jumps is no longer needed (I got the same results in a recent test using version 4.5.1). 4. What I would do to calculate D as funtion to the distance to the membrane protein is generate different index files containing lipids according to this distance (and hoping they don't move a lot during the simulation) and run different msd calculations. I think I have read in the mailing list about a script to make such a selection regarding distances to construct the index file or just make your own one. Good luck Javier El 02/12/10 12:50, Ángel Piñeiro escribió: I want to add that the MSD as a function of time (msd.xvg file) looks completely linear Greetings, Ángel Piñeiro. On Thu, 2010-12-02 at 12:45 +0100, Ángel Piñeiro wrote: Dear all, I aim to calculate the lateral diffusion coefficients of lipids as a function of the distance to a membrane protein using the Martini force field. For this I guess I could use the diff_mol.xvg output file of the g_msd command which provides the list of diffusion coefficients for each lipid (I guess the lipids are ordered as in the trajectory file). Then I would calculate the protein-lipid distance for each lipid and I would generate the diffusion vs distance file. Before starting the calculations on the membrane protein system I tested the g_msd command on a DPPC
Re: [gmx-users] Re: individual lateral diffusion coefficients
Dear Angel, I agree with Justin comments and I might add: Taken from the marrink-2004JPC martini paper: Microsecond simulations of the bilayer containing 256 DPPC molecules allows the observation of truely long time diffusive behavior. At T = 323 K, the lateral diffusion rates of DPPC equals 3 +/-1 10-7 cm2 s-1, of the same order of magnitude as experimentally measured (values are typically reported to be around 1 10-7 cm2 s-1 at temperatures close to 323 K; e.g., see refs 38 and 39) Here a factor 4 is used to scale the CG dynamics, your simulation is fine. I am however surprised by the variance of your individual lipids ... the length of your simulation might be the reason ... We have looked at lipid/protein interaction with Martini quite a lot and convergence is reached after a few microseconds and a multitude of exchanges of lipids between contacts with the protein and the bulk. You'd then have the issue of which lipid to consider in which section ... not a trivial choice. XAvier. On Dec 2, 2010, at 12:50 PM, Ángel Piñeiro wrote: I want to add that the MSD as a function of time (msd.xvg file) looks completely linear Greetings, Ángel Piñeiro. On Thu, 2010-12-02 at 12:45 +0100, Ángel Piñeiro wrote: Dear all, I aim to calculate the lateral diffusion coefficients of lipids as a function of the distance to a membrane protein using the Martini force field. For this I guess I could use the diff_mol.xvg output file of the g_msd command which provides the list of diffusion coefficients for each lipid (I guess the lipids are ordered as in the trajectory file). Then I would calculate the protein-lipid distance for each lipid and I would generate the diffusion vs distance file. Before starting the calculations on the membrane protein system I tested the g_msd command on a DPPC bilayer. In my bilayer simulation I removed the COM of lipids and water separately. Before analyzing it I removed jumps over the box boundaries using trjconv -pbc nojump and I created a index file with the PO4 atoms as a new group. Then I executed the following command: g_msd -s topol.tpr -f trajnojump.xtc -n p.ndx -lateral z -rmcomm from which I get the following output: D[ PO4] 0.0958 (+/- 0.0135) 1e-5 cm^2/s I think the value is not crazy for DPPC at 323 K using Martini... but I noticed that the D values for the independent lipids reported in the diff_mol.xvg file range from 0.0021959 to 0.482909 cm^2/s. If the differences are so high for a single lipid bilayer I suspect that I will not observe significant differences as a function of the distance to the protein in my simulations of the whole system... probably I am doing something wrong¿? Thanks for any advice Ángel Piñeiro. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Note on oscillation period / time step
El 02/12/10 19:02, Justin A. Lemkul escribió: Javier Cerezo wrote: Hello. It looks like you're missing the bonded-interactions parameters. [ bonds ] ; aiaj funct *R0 Kb *121 * XX* 131 * XX* 141 * XX* 151 * XX* 561 * XX* (also angles...) Is it implicit somewhere? I don't know if it is automatic and if so, from where the parameters are taken. If it is by using atoms names and the ffbonded.itp from oplsaa, then atom name OA is missing in the itp file. I think that, according to the code (grompp.c), this note may arise if the force constants are zero. Atom types are interpolated from ffbonded.itp and assigned. If the problem were in the bonded parameters, a very different fatal error arises. There is no problem here. I see it now, the stimated frequency fits with the force constat in ffbonded.itp and masses in ffnonbonded.itp. Thanks (That's a nice new check in grompp, by the way.) -Justin Javier El 02/12/10 17:11, Robin C. Underwood escribió: GMX Users: When I run grompp on methanol in water in v. 4.5.3 I get the following Note: NOTE 1 [file methanol.top, line 73]: The bond in molecule-type MET between atoms 5 OA and 6 HO has an estimated oscillational period of 9.0e-03 ps, which is less than 10 times the time step of 1.0e-03 ps. Maybe you forgot to change the constraints mdp option. Here is my mdp file: ;User Robin ;Wed Dec.1 2010 ;Input file ; title = Yo cpp = /lib/cpp integrator = md dt = 0.001; ps ! nsteps = 110; total 1000 ps=1 ns nstcomm = 10 ; (x) coordinates, (v) is velocities, (f) is forces ; This affects traj.trr ; these numbers shouldn't be too small (100,000), takes up disk space nstxout = 1000 nstvout = 1000 nstfout = 1000 ; Output frequency for energies nstlog = 100 nstenergy = 100 ; This affects .xtc file for movies this should be a fairly small number nstxtcout = 100 xtc-precision = 1000 ; parameters for neighbors nstlist = 10 ns_type = grid rlist = 0.9 ; electrostatics coulombtype= pme pme_order= 4 ewald_rtol = 1e-5 ewald_geometry = 3d epsilon_surface = 0 fourierspacing= 0.1 fourier_nx = 0.0 fourier_ny = 0.0 fourier_nz = 0.0 rcoulomb= 0.9 optimize_fft= yes Dispcorr= EnerPres vdwtype= cutoff rvdw_switch= 0.85 rvdw= 0.9 ; Berendsen temperature coupling is on in two groups Tcoupl = v_rescale tc-grps= system tau_t = 0.1 ref_t = 300 ; Energy monitoring energygrps = MET SOL ; Isotropic pressure coupling is now on Pcoupl = berendsen Pcoupltype = isotropic tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is off at 300 K. gen_vel = no gen_temp= 300.0 gen_seed= 173529 Here is my top file: ; ; ; Include forcefield parameters #include ffoplsaa.itp ; ; Methanol, Jorgensen et al. JACS 118 pp. 11225 (1996) ; [ moleculetype ] ; name nrexcl MET3 [ atoms ] ; nrtype resnr residuatomcgnr charge mass 1 opls_157 1 METC 10.145 2 opls_156 1 METH 10.04 3 opls_156 1 METH 10.04 4 opls_156 1 METH 10.04 5 opls_154 1 MET OA 1-0.683 6 opls_155 1 MET HO 10.418 [ bonds ] ; aiaj funct c0 c1 121 131 141 151 561 [ pairs ] ; ijfunct 26 36 46 [ angles ] ; aiajak funct c0c1 ; H3 2151 315 1 4151 4 1 3 1 4121 [ system ] ; Name MET in water [ molecules ] ; Compound#mols MET 1 SOL503 Do I need to add some sort of constraint on my methanol molecule? Thanks, Robin -- Javier CEREZO BASTIDA Estudiante de Doctorado - Dpto. Química-Física Universidad de Murcia 30100 MURCIA (España) Tlf.(+34)868887434 -- Javier CEREZO BASTIDA Estudiante de Doctorado - Dpto. Química-Física Universidad de Murcia 30100 MURCIA (España) Tlf.(+34)868887434 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before
[gmx-users] Re: Note on oscillation period / time step
Thanks for all the responses. After rechecking my top and manually inputting the [ ...types ] fields, the note remains. It is not clear to me whether I need to modify my top file or add some additional constraint (either in the top or mdp). Is it OK to have a bond oscillation period of this magnitude relative to my timestep? I've not seen this note in previous versions. Robin Javier Cerezo wrote: Hello. It looks like you're missing the bonded-interactions parameters. [ bonds ] ; aiaj funct *R0 Kb *12 1 * XX* 1 3 1 * XX* 1 4 1 * XX* 1 5 1 * XX* 5 6 1 * XX* (also angles...) Is it implicit somewhere? I don't know if it is automatic and if so, from where the parameters are taken. If it is by using atoms names and the ffbonded.itp from oplsaa, then atom name OA is missing in the itp file. I think that, according to the code (grompp.c), this note may arise if the force constants are zero. Atom types are interpolated from ffbonded.itp and assigned. If the problem were in the bonded parameters, a very different fatal error arises. There is no problem here. -Justin Javier El 02/12/10 17:11, Robin C. Underwood escribió: GMX Users: When I run grompp on methanol in water in v. 4.5.3 I get the following Note: NOTE 1 [file methanol.top, line 73]: The bond in molecule-type MET between atoms 5 OA and 6 HO has an estimated oscillational period of 9.0e-03 ps, which is less than 10 times the time step of 1.0e-03 ps. Maybe you forgot to change the constraints mdp option. Here is my mdp file: ;User Robin ;Wed Dec.1 2010 ;Input file ; title = Yo cpp = /lib/cpp integrator = md dt = 0.001 ; ps ! nsteps = 110 ; total 1000 ps=1 ns nstcomm = 10 ; (x) coordinates, (v) is velocities, (f) is forces ; This affects traj.trr ; these numbers shouldn't be too small (100,000), takes up disk space nstxout = 1000 nstvout = 1000 nstfout = 1000 ; Output frequency for energies nstlog = 100 nstenergy = 100 ; This affects .xtc file for movies this should be a fairly small number nstxtcout = 100 xtc-precision = 1000 ; parameters for neighbors nstlist = 10 ns_type = grid rlist = 0.9 ; electrostatics coulombtype = pme pme_order= 4 ewald_rtol = 1e-5 ewald_geometry = 3d epsilon_surface = 0 fourierspacing = 0.1 fourier_nx = 0.0 fourier_ny = 0.0 fourier_nz = 0.0 rcoulomb= 0.9 optimize_fft= yes Dispcorr = EnerPres vdwtype = cutoff rvdw_switch = 0.85 rvdw= 0.9 ; Berendsen temperature coupling is on in two groups Tcoupl = v_rescale tc-grps = system tau_t = 0.1 ref_t = 300 ; Energy monitoring energygrps = MET SOL ; Isotropic pressure coupling is now on Pcoupl = berendsen Pcoupltype = isotropic tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is off at 300 K. gen_vel = no gen_temp= 300.0 gen_seed= 173529 Here is my top file: ; ; ; Include forcefield parameters #include ffoplsaa.itp ; ; Methanol, Jorgensen et al. JACS 118 pp. 11225 (1996) ; [ moleculetype ] ; name nrexcl MET 3 [ atoms ] ; nrtype resnr residuatomcgnrcharge mass 1 opls_157 1 METC 1 0.145 2 opls_156 1 METH 1 0.04 3 opls_156 1 METH 1 0.04 4 opls_156 1 METH 1 0.04 5 opls_154 1 MET OA 1 -0.683 6 opls_155 1 MET HO 1 0.418 [ bonds ] ; aiaj funct c0 c1 12 1 13 1 14 1 15 1 56 1 [ pairs ] ; i j funct 26 36 46 [ angles ] ; aiajak funct c0c1 ; H3 2 1 5 1 3 1 5 1 4 1 5 1 4 1 31 4 1 2 1 [ system ] ; Name MET in water [ molecules ] ; Compound#mols MET 1 SOL 503 Do I need to add some sort of constraint on my methanol molecule? Thanks, Robin -- Javier CEREZO BASTIDA Estudiante de Doctorado - Dpto. Química-Física Universidad de Murcia 30100 MURCIA (España)
RE: [gmx-users] Re: individual lateral diffusion coefficients
It seems to me that it will be for the reasons mentioned in the paper http://dx.doi.org/10.1063/1.2393240 http://dx.doi.org/10.1063/1.2393240 By focusing on the phosphate atom, you are measuring the actual movement of the entire lipid molecule within the membrane, which is the diffusion that is measured typically experimentally. If you use the entire molecule, then you get the movement of the alkane chains as well, which increase the diffusion coefficient by more than a factor of ten. Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@monash.edu +61 3 9903 9304 - When the only tool you own is a hammer, every problem begins to resemble a nail. From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Javier Cerezo Sent: Friday, 3 December 2010 2:46 AM To: gmx-users@gromacs.org Subject: Re: [gmx-users] Re: individual lateral diffusion coefficients Sorry for the misspell... Thanks Justin. Do you know the reason behind? I am trying following that protocol and my P curve in not as linear as All-lipid-atoms one (DPPC, FF: G53a6, t=50ns). Furthermore, regarding the linear region, the slopes are not the same. So which one do you think is more accurate? Thanks again Javier El 02/12/10 16:09, Justin A. Lemkul escribió: Ángel Piñeiro wrote: Hi Javier I think I saw this in several mails of this list and it is also implicit in the Justin tutorial for analysis of bilayers. I am not sure whether or not this has also been published... I do not remember any paper. I think this is reasonable for lipids in contact with membrane proteins because only a part of the lipid could be tied to the protein... then the diffusion for different parts of the lipid could be different. I think I will calculate the diffusion for each lipid individually... If you are interested in comparing results you could contact me off the list. I haven't followed this thread at all, but I saw my name come up :) This is what I have always based my g_msd calculations on: http://lists.gromacs.org/pipermail/gmx-users/2008-January/031804.html -Justin Saludos, Ángel. On Thu, 2010-12-02 at 14:22 +0100, Javier Cerezo wrote: Hi Ángel Can you provide a citation about the use of only PO4 atoms to calculate the diffusion constant? Is it always recommended or just with CG simulations? I'm also working on diffusion calculation and that will be interesting. By the way, regarding the index files I mentioned, it might be better to have a group of lipids that are at a certain distance from the protein in the same index, again to improve sampling (maybe this is not a way to improve sampling, I don't know). Thanks Javier El 02/12/10 13:56, Ángel Piñeiro escribió: Hi Javier 1.- you are right! the diff_mol.xvg file I reported was from a previous attempt in which I used the whole lipid molecules with the -mol option on, instead of the PO4 beads with -mol off. Sorry for this confusion 2.- As I said above, I did attempts using both the whole molecule and the PO4 beads. Yes I saw the figure 6 in the Wolhert Edholm's paper but I read in several other references that the calculation is more accurate by using only the P atom... what makes sense to me mainly for the lipids which are in contact with proteins 3.- I agree that removing jumps does not change anything. I decided to give this information in my message to avoid a reply saying try to remove jumps ;) 4.- Yes I agree that I could do the calculation by creating an index for each lipid... I guess that is the safest way to proceed... Thanks for your reply! Ángel. On Thu, 2010-12-02 at 13:30 +0100, Javier Cerezo wrote: Hello Ángel. Well, there are a some things that I don't understand about your calculation, but might be just a problem of mine. Here you have my comments: 1. How do you get the diff_mol.xvg file if you are not using -mol in your command line input (and you index file has broken molecules). 2. Why do you select just an atom to calculate the diffusion? According to Wolhert and Edholm (JCP, 125, 204703) the MSD for all lipids atoms reach the same slope, so I guess using them all could improve sampling (I'm not sure). 3. I think that reprocessing of your trajectory to remove jumps is no longer needed (I got the same results in a recent test using version 4.5.1). 4. What I would do to calculate D as funtion to the distance to the membrane protein is generate different index files containing lipids according to this distance (and hoping they don't move a lot during the simulation) and run different msd calculations. I think I have read in the mailing list about a script to make such a selection regarding distances to construct the index file or just make your own one. Good luck
Re: [gmx-users] Re: individual lateral diffusion coefficients
Hi. I think that these arguments are given for short-time diffusion (D1). But at larger times all MSD curves reach the same slope, so all of them have the same brownian diffusion (D2). Then, I wonder if taking all the atoms, which means more points to average, will results in better statistics and thus better results (even for not such a long times). Does it make sense or am I overseeing fundamental physical meaning? Thanks Javier Dallas Warren escribió: It seems to me that it will be for the reasons mentioned in the paper http://dx.doi.org/10.1063/1.2393240 http://dx.doi.org/10.1063/1.2393240 By focusing on the phosphate atom, you are measuring the actual movement of the entire lipid molecule within the membrane, which is the diffusion that is measured typically experimentally. If you use the entire molecule, then you get the movement of the alkane chains as well, which increase the diffusion coefficient by more than a factor of ten. Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@monash.edu +61 3 9903 9304 - When the only tool you own is a hammer, every problem begins to resemble a nail. *From:* gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] *On Behalf Of *Javier Cerezo *Sent:* Friday, 3 December 2010 2:46 AM *To:* gmx-users@gromacs.org *Subject:* Re: [gmx-users] Re: individual lateral diffusion coefficients Sorry for the misspell... Thanks Justin. Do you *know* the reason behind? I am trying following that protocol and my P curve in not as linear as All-lipid-atoms one (DPPC, FF: G53a6, t=50ns). Furthermore, regarding the linear region, the slopes are not the same. So which one do you think is more accurate? Thanks again Javier El 02/12/10 16:09, Justin A. Lemkul escribió: Ángel Piñeiro wrote: Hi Javier I think I saw this in several mails of this list and it is also implicit in the Justin tutorial for analysis of bilayers. I am not sure whether or not this has also been published... I do not remember any paper. I think this is reasonable for lipids in contact with membrane proteins because only a part of the lipid could be tied to the protein... then the diffusion for different parts of the lipid could be different. I think I will calculate the diffusion for each lipid individually... If you are interested in comparing results you could contact me off the list. I haven't followed this thread at all, but I saw my name come up :) This is what I have always based my g_msd calculations on: http://lists.gromacs.org/pipermail/gmx-users/2008-January/031804.html -Justin Saludos, Ángel. On Thu, 2010-12-02 at 14:22 +0100, Javier Cerezo wrote: Hi Ángel Can you provide a citation about the use of only PO4 atoms to calculate the diffusion constant? Is it always recommended or just with CG simulations? I'm also working on diffusion calculation and that will be interesting. By the way, regarding the index files I mentioned, it might be better to have a group of lipids that are at a certain distance from the protein in the same index, again to improve sampling (maybe this is not a way to improve sampling, I don't know). Thanks Javier El 02/12/10 13:56, Ángel Piñeiro escribió: Hi Javier 1.- you are right! the diff_mol.xvg file I reported was from a previous attempt in which I used the whole lipid molecules with the -mol option on, instead of the PO4 beads with -mol off. Sorry for this confusion 2.- As I said above, I did attempts using both the whole molecule and the PO4 beads. Yes I saw the figure 6 in the Wolhert Edholm's paper but I read in several other references that the calculation is more accurate by using only the P atom... what makes sense to me mainly for the lipids which are in contact with proteins 3.- I agree that removing jumps does not change anything. I decided to give this information in my message to avoid a reply saying try to remove jumps ;) 4.- Yes I agree that I could do the calculation by creating an index for each lipid... I guess that is the safest way to proceed... Thanks for your reply! Ángel. On Thu, 2010-12-02 at 13:30 +0100, Javier Cerezo wrote: Hello Ángel. Well, there are a some things that I don't understand about your calculation, but might be just a problem of mine. Here you have my comments: 1. How do you get the diff_mol.xvg file if you are not using -mol in your command line input (and you index file has broken molecules). 2. Why do you select just an atom to calculate the diffusion? According to Wolhert and Edholm (JCP, 125, 204703) the MSD for all lipids atoms reach the same slope, so I guess using them all could improve sampling (I'm not sure). 3. I think that reprocessing of your trajectory to remove jumps is no longer needed (I got the same results in a
[gmx-users] creat .gro; select force field
Hi users: I run pure water MD. I need to run different water models. How can i get spce.gro, which means how can i get .gro of spce water? How can i get .gro of TIP4P? If i select TIP4P water model, which force field should i select? you know, i need .top, and .top should include force field. If i select SPCE water model, which force field should i select? I can find a spc216.gro, which is default solvent. I can use genbox to generate a box of solvent (spc water). how can we use other solvent, so we need to have the .gro of the solvent. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] cumulative numbers or running coordination numbers ?
Hi all, What is the standard designation (if any exists) of the function that is calculated using g_rdf -cn? Cumulative numbers? Running coordination numbers? Which of them is better to be used in the article? Thanks for your insights. Vitaly Dr. Vitaly V. Chaban| skype: vvchaban Department of Chemistry | email: v.cha...@rochester.edu University of Rochester | email: vvcha...@gmail.com Rochester, NY 14627-0216 | email: cha...@univer.kharkov.ua United States of America | WWW: chem.rochester.edu/~prezhdo_group/ -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] tpbconv -zeroq results all coulombic energies to zero
Hi, all: I was trying to use tpbconv to modify the tpr file with the command: tpbconv -s %s.tpr -nsteps -1 -zeroq -n index -o final.tpr It basically sets the charge of one group to zero. However, when I perform mdrun -rerun, all the coulombic energies are zeros, i.e., Coulomb-(SR), Coul.-recip. This really does not make sense since I still have atoms in other groups that are charged. I was using gromacs4.0.7. Has anyone seen this before? What exactly is the correct way to zeroize the charge for a group of atoms? Thanks, Bin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] tpbconv -zeroq results all coulombic energies to zero
On 2010-12-03 08.45, BIN ZHANG wrote: Hi, all: I was trying to use tpbconv to modify the tpr file with the command: tpbconv -s %s.tpr -nsteps -1 -zeroq -n index -o final.tpr It basically sets the charge of one group to zero. However, when I perform mdrun -rerun, all the coulombic energies are zeros, i.e., Coulomb-(SR), Coul.-recip. This really does not make sense since I still have atoms in other groups that are charged. I was using gromacs4.0.7. Please check using gmxdump that there still are charged groups left in your tpr file. Has anyone seen this before? What exactly is the correct way to zeroize the charge for a group of atoms? Thanks, Bin -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://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/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
