[gmx-users] Ion conduction through a protein-membrane system
Dear users, I want to study ion conduction through a protein-memrane system. First of all, I tried to simulate a usual protein-membrane system. I'd like to know if it is possible to add asymmetrical number of ions to leaflets of membrane? Secondly, is it possible to apply an external electrical field to study ion conduction in a system? Thanks in advance. Sincerely, Shima -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] pdb2gmx with more than 9999 residues
A pdb file with a resid exceeds the proper PDB format. You can resolvate a dry lipid bilayer using genbox fine; I don't know what problem you have with the solvation and minimization using that method, http://manual.gromacs.org/current/online/genbox.html You can also pdb2gmx or editconf the lipids and water separately as you suggested, then merge the files and run ediconf on the merged file to renumber the atoms. On 2012-10-02 02:16:00PM +0800, Jernej Zidar wrote: Hi. I'm trying to import a solvated lipid bilayer (cholesterol+POPC+water) I generated in CHARMM but I have a problem with pdb2gmx unwilling to accept the segment containing water molecules. It does import everything seemingly correctly, yet when one examines the resulting .gro file, he can see that the system does not accept more than residues/segment: residue 1 becomes 1000 and so on. Now, what can one do ammend the current situation? One option would be to import only the lipid part of the system and then solvate it again in GROMACS, but that path is not really useful because it doesn't allow to fine tune the amount and location of water molecules. I tried this option but it doesn't work in my case as there's a gaping hole between the water layer and the lipids, that cause the minimization to essentially fail. Another option would be to import the lipid and water part separately but this would again cause problems with atom numbering when both segments would be combined together. Manually editing the PDB file is not an option as the PDB file has ~80.000 lines. Any other way? I'm using GROMACS 4.5.5 on Ubuntu 12.04 64-bit. Thanks in advance, Jernej -- 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 -- == Peter C. Lai| University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu| Birmingham AL 35294-4461 (205) 690-0808 | == -- 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] Ion conduction through a protein-membrane system
On 2012-10-01 11:16:43PM -0700, Shima Arasteh wrote: Dear users, I want to study ion conduction through a protein-memrane system. First of all, I tried to simulate a usual protein-membrane system. I'd like to know if it is possible to add asymmetrical number of ions to leaflets of membrane? Yes. You need to first use trjorder -z to reorder the waters, then you need to make 2 index group of consecutive atoms in each layer. Tell genion to only pick waters from the separate index groups. It is important that the index groups representing the water surrounding the top and bottom leaflet are consecutive in atom number or else genion will refuse to run. The easiest way to do that is to find Z around the middle of the bilayer where there are no waters and separate the top waters from the bottom waters. Note that use of pbc=xyz Periodic Boundary Conditions will allow the extracellular ions to travel into the intracellular space as the top ions diffuse +Z (and the intracellular ions can diffuse -Z into the extracellular space), so track your ion movements appropriately. Finally if the total charge of the system isn't balanced, grompp will throw a notice or a warning. I don't know what the consequences of running a simulation of a non-neutral system has on things like energy conservation... Secondly, is it possible to apply an external electrical field to study ion conduction in a system? The manual appears suggests such a thing might be possible to some extent. You'll probably want to look for yourself to see if your use-case is supported. -- == Peter C. Lai| University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu| Birmingham AL 35294-4461 (205) 690-0808 | == -- 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] Ion conduction through a protein-membrane system
Hi Shima, there is also a patch for Gromacs available to study ion conduction through membrane channels that you might find useful. Please take a look at this page: http://www.mpibpc.mpg.de/grubmueller/compel Best, Carsten On Oct 2, 2012, at 8:16 AM, Shima Arasteh shima_arasteh2...@yahoo.com wrote: Dear users, I want to study ion conduction through a protein-memrane system. First of all, I tried to simulate a usual protein-membrane system. I'd like to know if it is possible to add asymmetrical number of ions to leaflets of membrane? Secondly, is it possible to apply an external electrical field to study ion conduction in a system? Thanks in advance. Sincerely, Shima -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- 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/grubmueller/kutzner -- 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] Ion conduction through a protein-membrane system
Thanks Casten. Sincerely, Shima - Original Message - From: Carsten Kutzner ckut...@gwdg.de To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Tuesday, October 2, 2012 11:02 AM Subject: Re: [gmx-users] Ion conduction through a protein-membrane system Hi Shima, there is also a patch for Gromacs available to study ion conduction through membrane channels that you might find useful. Please take a look at this page: http://www.mpibpc.mpg.de/grubmueller/compel Best, Carsten On Oct 2, 2012, at 8:16 AM, Shima Arasteh shima_arasteh2...@yahoo.com wrote: Dear users, I want to study ion conduction through a protein-memrane system. First of all, I tried to simulate a usual protein-membrane system. I'd like to know if it is possible to add asymmetrical number of ions to leaflets of membrane? Secondly, is it possible to apply an external electrical field to study ion conduction in a system? Thanks in advance. Sincerely, Shima -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- 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/grubmueller/kutzner -- 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] Ion conduction through a protein-membrane system
Thanks Peter for your explanation. Sincerely, Shima - Original Message - From: Peter C. Lai p...@uab.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Tuesday, October 2, 2012 10:10 AM Subject: Re: [gmx-users] Ion conduction through a protein-membrane system On 2012-10-01 11:16:43PM -0700, Shima Arasteh wrote: Dear users, I want to study ion conduction through a protein-memrane system. First of all, I tried to simulate a usual protein-membrane system. I'd like to know if it is possible to add asymmetrical number of ions to leaflets of membrane? Yes. You need to first use trjorder -z to reorder the waters, then you need to make 2 index group of consecutive atoms in each layer. Tell genion to only pick waters from the separate index groups. It is important that the index groups representing the water surrounding the top and bottom leaflet are consecutive in atom number or else genion will refuse to run. The easiest way to do that is to find Z around the middle of the bilayer where there are no waters and separate the top waters from the bottom waters. Note that use of pbc=xyz Periodic Boundary Conditions will allow the extracellular ions to travel into the intracellular space as the top ions diffuse +Z (and the intracellular ions can diffuse -Z into the extracellular space), so track your ion movements appropriately. Finally if the total charge of the system isn't balanced, grompp will throw a notice or a warning. I don't know what the consequences of running a simulation of a non-neutral system has on things like energy conservation... Secondly, is it possible to apply an external electrical field to study ion conduction in a system? The manual appears suggests such a thing might be possible to some extent. You'll probably want to look for yourself to see if your use-case is supported. -- == Peter C. Lai | University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu | Birmingham AL 35294-4461 (205) 690-0808 | == -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- 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: Re: Binding Energy to Binding affinity (Kd) (Justin Lemkul)
Hi Justin, I used ~20 windows to sample ~2 nm pulling. I notice that the distance between the complex being increased during the pulling but not gradually. At the distance of 0-1nm, there are 70 snapshots (the distance sometime increased sometimes decreased). At the distance of 1-2nm, there are only 30 snapshots (the distance kept increasing always). At the distance more than 3nm, the distance increased as 0.3nm of each snapshot, is it normal and reliable? You mentioned error estimate for each replicate, but what is it? How to define it? For the conversion of energy to Kd, I standardized every unit into international unit and then calculated the Kd value. Here I post my formula: $ln=2.718281828459; ## constant $cal=4186; ## convert kcal into J $R=8.3144621; #J/(mol*K) ideal gas constant $mol=6.02214179*(10**23); ## mole numbers, constant $procon=9.494/15; ## the protein concentration based on ions' concentration. mol/ml $a=$energy*$cal/$t/$R; ## $energy here is the binding energy calculated from umbrella sampling (kcal/mol) $k=$ln**$a; $kd=1/$k *$procon * (10**9); ## Kd vs Ka; unit is μM here. Thank you, Jiangfeng. On 10/1/12 4:36 AM, Du Jiangfeng (BIOCH) wrote: Dear Everyone, I have two questions about the conversion of binding energy to binding affinity. I predicted the binding energy of a protein-membrane complex by umbrella sampling (based on Justin's tutorial). After sampling, the binding energy should be the substract of (min-max) PMF. I have repeated the simulation 12 times, and then I have done umbrella samplings also 12 times, then got 12 binding energies which varies from -200 Kcal/mol to -100kcal/mol, does the value vary too much? or is it reasonable since the simulation results can be different? Are those values too huge? Without an explanation of how long your windows are and what the error estimate for each replicate is, it is impossible to answer this question. When I tried to convert the binding energy to Kd by the formula deltaG=-RTlnK, I am frustrated by the kd value. If the binding energy is -100kcal/mol, the kd is calculated as 3.35e-59 ?M. The kd is 1.77e-126 ?M when binding energy is -200kcal/mol. This is impossible. But what is going wrong? I think you are doing your calculations incorrectly (I obtain your values when using units of kcal/mol for dG but kJ/mol-K for the gas constant - note the mismatch), but even when done properly, the values are still unreasonable. -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] g_energy menu choices inconsistent?
On 10/2/12 1:40 AM, Ladasky wrote: I have been trying to automate my simulation setup and monitoring. I wrote a script which calls g_energy, and automatically generates plots of potential energy from my EM step, temperature from my NVT equilibration step, and pressure and density from my NPT equilibration step. For each of these three simulations, it appeared that the numbering on the g_energy menu was consistent: Potential = 11, Temperature = 15, Pressure = 16, Density = 22. I wrote my program assuming that these numbers would always describe the parameters listed. Maybe not? Something is still going wrong with my production run, I'm getting a segmentation fault after about 40,000 steps (sigh, I almost thought I had this whole setup understood and debugged). So I used my graphing program to check the temperature, and the results were... odd, bouncing from +300 to -100. The values in my MD.log file disagreed with my graph, they were all within a few degrees of 310K, my target temperature. So I re-ran g_energy directly, bypassing my program, using my production-run ener.edr file as input. The menu showed: Potential = 10, Temperature = 13, Pressure = 15, Density = 21. Seeing this number shift, I understand why my temperature graph for the production looked wrong -- I was actually graphing pressure. Not knowing what menu options to expect will impair my ability to automate the running of g_energy. I can try some tricks to capture that menu each time I run the program, but it will be a chore. I would also like to understand: what is the REASON that these numbers might change between runs? Not all energy terms are written if they are not applicable. This saves disk space by making the .edr file smaller if it can be. Note that you can always select by name rather than number, i.e.: echo Temperature | g_energy -f ener.edr -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Please help
Hi everybody, I am still in confusion in which thermostat my be good for NPT MD calcualtions with protein and DNA. V-rescale, berenseden, Nose-hoover; parinello-rahman thermostats. Is the temperature and pressure coupling will be similar or different. Thanking in advance, With reagards Anik Anik Sen Student CSIR-Central Salt Marine Chemicals Research Institute, Gijubhai Badheka Marg. Bhavnagar, Gujarat 364002 [www.csmcri.org] -- 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] Please help
On 10/2/12 5:20 AM, Anik Sen wrote: Hi everybody, I am still in confusion in which thermostat my be good for NPT MD calcualtions with protein and DNA. V-rescale, berenseden, Nose-hoover; parinello-rahman thermostats. Is the temperature and pressure coupling will be similar or different. The different algorithms will lead to different distributions for temperature and pressure values. What does your reading of the primary literature for these algorithms tell you? What methods do others use when simulating similar systems? What does your searching of the list archive turn up? Hint: we discuss this type of thing a lot, so there's plenty in the archive from which to learn. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: Possible bug in the temperature calculation from rerun
Dear gmxusers,
Thank you for your answers so far. I have run a few more test rerun and here
is what I got:
-The number of degree of freedom are the same whatever the topology I run
with, both in the log file and from the grompp output.
-Comparing the trajectories created from rerun with gmxdump and diff show
only minor differences, such as atoms positioned on one side or the other of
the simulation box. The velocities are strictly the same however. Here is an
example:
8836288,8836290c8836288,8836290
x[394728]={ 1.32183e+02, 3.15341e+00, 5.17869e+00}
x[394729]={ 1.32054e+02, 3.10839e+00, 5.14599e+00}
x[394730]={ 1.32314e+02, 3.17612e+00, 5.13366e+00}
---
x[394728]={-7.17163e-04, 3.15341e+00, 5.17869e+00}
x[394729]={-1.29196e-01, 3.10839e+00, 5.14599e+00}
x[394730]={ 1.29883e-01, 3.17612e+00, 5.13366e+00}
-If I use another topology where I only have the interaction with water
not set to zero (still with electrostatic), I get a temperature of ~326K
intermediate between the desired value of 325K and the value I got with all
the interaction shutdown of ~327K.
-Turning the temperature/pressure coupling on or off do not change the
results.
I think there is a problem in the calculation of the kinetic energy that
translate to the temperature. However setting all the interaction but the
electrostatic to zero should not modify the kinetic energy calculated from
'mdrun -rerun'.
I do not know how to proceed from here, maybe I should post my mdp top and
log files here or on the developers forum ?
Have a good day,
Bastien Loubet
--
View this message in context:
http://gromacs.5086.n6.nabble.com/Possible-bug-in-the-temperature-calculation-from-rerun-tp5001194p5001508.html
Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
--
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: Re: Binding Energy to Binding affinity (Kd) (Justin Lemkul)
On 10/2/12 4:39 AM, Du Jiangfeng (BIOCH) wrote: Hi Justin, I used ~20 windows to sample ~2 nm pulling. I notice that the distance between the complex being increased during the pulling but not gradually. At the distance of 0-1nm, there are 70 snapshots (the distance sometime increased sometimes decreased). At the distance of 1-2nm, there are only 30 snapshots (the distance kept increasing always). At the distance more than 3nm, the distance increased as 0.3nm of each snapshot, is it normal and reliable? I will assume you are using a harmonic potential (umbrella) to do the pulling. In this case, your observations are totally normal. When two species interact strongly, it is harder to pull them apart, thus the spring extends further to induce a larger force before displacement occurs. As the restoring forces are overcome, it is easier to move the pulled group through solution, so it makes more steady progress as the molecules are separated. You mentioned error estimate for each replicate, but what is it? How to define it? g_wham has numerous options for statistical analysis. I would encourage you to read their full description in the g_wham paper, and at minimum, the short description in g_wham -h. For the conversion of energy to Kd, I standardized every unit into international unit and then calculated the Kd value. Here I post my formula: $ln=2.718281828459; ## constant $cal=4186; ## convert kcal into J $R=8.3144621; #J/(mol*K) ideal gas constant $mol=6.02214179*(10**23); ## mole numbers, constant $procon=9.494/15; ## the protein concentration based on ions' concentration. mol/ml This ends up being something like 633 M, which may well be correct based on size of the molecular system, but seems very odd to me. -Justin $a=$energy*$cal/$t/$R; ## $energy here is the binding energy calculated from umbrella sampling (kcal/mol) $k=$ln**$a; $kd=1/$k *$procon * (10**9); ## Kd vs Ka; unit is μM here. Thank you, Jiangfeng. On 10/1/12 4:36 AM, Du Jiangfeng (BIOCH) wrote: Dear Everyone, I have two questions about the conversion of binding energy to binding affinity. I predicted the binding energy of a protein-membrane complex by umbrella sampling (based on Justin's tutorial). After sampling, the binding energy should be the substract of (min-max) PMF. I have repeated the simulation 12 times, and then I have done umbrella samplings also 12 times, then got 12 binding energies which varies from -200 Kcal/mol to -100kcal/mol, does the value vary too much? or is it reasonable since the simulation results can be different? Are those values too huge? Without an explanation of how long your windows are and what the error estimate for each replicate is, it is impossible to answer this question. When I tried to convert the binding energy to Kd by the formula deltaG=-RTlnK, I am frustrated by the kd value. If the binding energy is -100kcal/mol, the kd is calculated as 3.35e-59 ?M. The kd is 1.77e-126 ?M when binding energy is -200kcal/mol. This is impossible. But what is going wrong? I think you are doing your calculations incorrectly (I obtain your values when using units of kcal/mol for dG but kJ/mol-K for the gas constant - note the mismatch), but even when done properly, the values are still unreasonable. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] RE: Gromacs 2 CHARMM
Dear All, Does anyone have a small script for converting Gromacs (GROMOS type) ff to CHARMM format, or an amino acid top file in CHARMM format for such. I have seen some scripts, but they work only with different topology types. Thought I would ask, otherwise I sit here for three days playing with text editors, Sincerely, Stephan Watkins -- 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] MPI simulation with CHARMM27 force field and CMAP dihedrals problem
Hi, I have tried to simulate a protein in water with the CHARMM27 force field and the GROMACS simulation package. Without the CMAP correction the simulation runs just fine, but when adding the CMAP correction to the dihedrals, the protein quickly starts to unfold and the simulation stops (with no error message in log or supercomputer's output file). I'm running my simulations on a supercomputer with 64 processors and I'm using mdrun_mpi. When running on my desktop with four cores I have no problems. Could it be that the current mpi version of mdrun in the supercomputer is the reason for this, or is the CMAP correction unavailable for parallel simulations using the mpi as in the case of GPUs when using an implicit solvent model? Best regards, Artturi Koivuniemi -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] umbrella sampling (PMF) position discrepancy
Hello Gromacs users, The solution that ended up working is selecting a different pull_pbcatom0 from the reference group, the protein, such that the atom is approx. in the center of mass of the protein. I hope that others may find this useful, Thanks to Martin Vesper and Justin Lemkul for their insights, Raphael On Tue, Sep 11, 2012 at 5:22 PM, Raphael Alhadeff raphael.alhad...@mail.huji.ac.il wrote: Thank you all for your help, Sheeba- Yes, I get both positive and negative results. I think what you describe is what I would get if I used 'distance' for the geometry. In any case, I have values from +2 to about -3, and they are not evenly distributed (unlike the coordinates, which are more or less evenly distributed) but are rather highly packed around -1 and then get increasingly farther away from each other. Jianguo- I did not see that thread before, I read it now but could not find anything to solve my problem. Justin- Thank you very much for your willingness to help, I will send the files promptly. Thanks again to everyone, I will post again should we find the problem and solution for anyone who might find it useful.. Raphael -- 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] Regarding g_cluster process MPI enabled
Dear Friends, Gromacs script such as g_cluster takes lot of time to complete in a single machine. Is their any way to give this job to a cluster machine like mdrun. Since mdrun is MPI enabled so I can easily execute it on cluster. Anybody in group have any clue that how we can execute g_cluster command on a cluster machine ? regards Vidya -- 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] Regarding g_cluster process MPI enabled
Hi... you have to implement the algorithm using parallel paradigma (MPI, openmp, thread) Alternatively, there is a workaround to bypass the serial rmsd matrix building (the most time consuming part). g_cluster reads a rmsd matrix as input, you can run different rmsd instance in parallel, using appropriate input, in order to obtain the different rows of the matrix. Next, you have to collect these outputs through in order to have the .xpm file through an appropriate script (that you have to write). This matrix can be used as input to g_cluster that will use it to calculate clusters Francesco 2012/10/2 R.Vidya Rajendran (10PHD013) vidya2...@vit.ac.in Dear Friends, Gromacs script such as g_cluster takes lot of time to complete in a single machine. Is their any way to give this job to a cluster machine like mdrun. Since mdrun is MPI enabled so I can easily execute it on cluster. Anybody in group have any clue that how we can execute g_cluster command on a cluster machine ? regards Vidya -- 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 -- Cordiali saluti, Dr.Oteri Francesco -- 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] g_energy menu choices inconsistent?
On 02/10/12 11:53, Justin Lemkul wrote: Note that you can always select by name rather than number, i.e.: echo Temperature | g_energy -f ener.edr Didn't know that, this really saves me a lot of trouble! Thanks Justin! m. -- Massimo Sandal, Ph.D. http://devicerandom.org -- 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] Density measurment
On 10/2/12 7:07 AM, rama david wrote: Hi Gromacs Users, I did simulation of two random coil peptides for 100ns. after 70 ns these peptide get converted to anti parallel beta sheet structure. I am interested to see the water density in between these peptideswith respect to time change and also the no of water molecule between the peptide with respect to time. And at the same time the distance between the peptide.. I need these information in xvg graph. I found out the distance between peptide by g_mindist but I not found the appropriate way to calculate density of water with respect to time between two peptides.. I used g_density but it not gave me the information as per my need. There are a variety of options in g_density that might work, like changing the direction along which the box is sliced, the interval of time examined, etc. I can envision this working quite well. g_densmap can do similar functions, and g_rdf can probably provide you with some useful information as well. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] what is theta in g_helixorient?
hello guys: I am using g_helixorient to analyze the helix property in my system and it generate three theta[1,2,3].xvg file. I am wondering what's that? I didn't find any comments in the help file. thanks Albert -- 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] what is theta in g_helixorient?
On 10/2/12 11:13 AM, Albert wrote: hello guys: I am using g_helixorient to analyze the helix property in my system and it generate three theta[1,2,3].xvg file. I am wondering what's that? I didn't find any comments in the help file. Have you read the last paragraph of g_helixorient -h? -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] error in grompp
Sir, I am studying the dynamics of membrane proteins using KALP-15 in DPPC. But grompp (before minimization of system_inflated.gro) giving error like this.. Fatal error: Atomtype LC3 not found Actually what changes I should do on the system topology, before grompp? I found that atomtype LC3 is found in my dppc.itp file. -- 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] error in grompp
On 10/2/12 11:26 AM, Shine A wrote: Sir, I am studying the dynamics of membrane proteins using KALP-15 in DPPC. But grompp (before minimization of system_inflated.gro) giving error like this.. Fatal error: Atomtype LC3 not found Actually what changes I should do on the system topology, before grompp? I found that atomtype LC3 is found in my dppc.itp file. If you're following my tutorial, then you have skipped a step or not completed the force field modifications. Go back and ensure that ffnonbonded.itp has been modified correctly to include the atom types and parameters from lipid.itp. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] what is theta in g_helixorient?
On 10/02/2012 05:16 PM, Justin Lemkul wrote: On 10/2/12 11:13 AM, Albert wrote: hello guys: I am using g_helixorient to analyze the helix property in my system and it generate three theta[1,2,3].xvg file. I am wondering what's that? I didn't find any comments in the help file. Have you read the last paragraph of g_helixorient -h? -Justin of course, here it is. I don't find anything related to my questions. Option Filename Type Description -s topol.tpr InputRun input file: tpr tpb tpa -f traj.xtc InputTrajectory: xtc trr trj gro g96 pdb cpt -n index.ndx Input, Opt. Index file -oaxis helixaxis.dat Output Generic data file -ocenter center.dat Output Generic data file -orise rise.xvg Output xvgr/xmgr file -oradius radius.xvg Output xvgr/xmgr file -otwist twist.xvg Output xvgr/xmgr file -obendingbending.xvg Output xvgr/xmgr file -otilt tilt.xvg Output xvgr/xmgr file -orot rotation.xvg Output xvgr/xmgr file Option Type Value Description -- -[no]h bool yes Print help info and quit -[no]version bool no Print version info and quit -niceint19 Set the nicelevel -b time 0 First frame (ps) to read from trajectory -e time 0 Last frame (ps) to read from trajectory -dt time 0 Only use frame when t MOD dt = first time (ps) -xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none -[no]sidechain bool no Calculate sidechain directions relative to helix axis too. -[no]incremental bool no Calculate incremental rather than total rotation/tilt. -- 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] what is theta in g_helixorient?
On 10/2/12 11:35 AM, Albert wrote: On 10/02/2012 05:16 PM, Justin Lemkul wrote: On 10/2/12 11:13 AM, Albert wrote: hello guys: I am using g_helixorient to analyze the helix property in my system and it generate three theta[1,2,3].xvg file. I am wondering what's that? I didn't find any comments in the help file. Have you read the last paragraph of g_helixorient -h? -Justin of course, here it is. I don't find anything related to my questions. Option Filename Type Description -s topol.tpr InputRun input file: tpr tpb tpa -f traj.xtc InputTrajectory: xtc trr trj gro g96 pdb cpt -n index.ndx Input, Opt. Index file -oaxis helixaxis.dat Output Generic data file -ocenter center.dat Output Generic data file -orise rise.xvg Output xvgr/xmgr file -oradius radius.xvg Output xvgr/xmgr file -otwist twist.xvg Output xvgr/xmgr file -obendingbending.xvg Output xvgr/xmgr file -otilt tilt.xvg Output xvgr/xmgr file -orot rotation.xvg Output xvgr/xmgr file Option Type Value Description -- -[no]h bool yes Print help info and quit -[no]version bool no Print version info and quit -niceint19 Set the nicelevel -b time 0 First frame (ps) to read from trajectory -e time 0 Last frame (ps) to read from trajectory -dt time 0 Only use frame when t MOD dt = first time (ps) -xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none -[no]sidechain bool no Calculate sidechain directions relative to helix axis too. -[no]incremental bool no Calculate incremental rather than total rotation/tilt. This is not the content to which I was referring. There are input/output options. The last paragraph of the help description is as follows: The tilt/rotation is calculated from Euler rotations, where we define the helix axis as the local x-axis, the residues/Calpha vector as y, and the z-axis from their cross product. We use the Euler Y-Z-X rotation, meaning we first tilt the helix axis (1) around and (2) orthogonal to the residues vector, and finally apply the (3) rotation around it. For debugging or other purposes, we also write out the actual Euler rotation angles as theta[1-3].xvg I believe this answers your question. Some help descriptions are quite long and the information you need may pass by in the terminal. Everything contained in the help description for all tools is also printed in the manual. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] what is theta in g_helixorient?
IC. thanks a lot for kind comments. On 10/02/2012 05:38 PM, Justin Lemkul wrote: On 10/2/12 11:35 AM, Albert wrote: On 10/02/2012 05:16 PM, Justin Lemkul wrote: On 10/2/12 11:13 AM, Albert wrote: hello guys: I am using g_helixorient to analyze the helix property in my system and it generate three theta[1,2,3].xvg file. I am wondering what's that? I didn't find any comments in the help file. Have you read the last paragraph of g_helixorient -h? -Justin of course, here it is. I don't find anything related to my questions. Option Filename Type Description -s topol.tpr InputRun input file: tpr tpb tpa -f traj.xtc InputTrajectory: xtc trr trj gro g96 pdb cpt -n index.ndx Input, Opt. Index file -oaxis helixaxis.dat Output Generic data file -ocenter center.dat Output Generic data file -orise rise.xvg Output xvgr/xmgr file -oradius radius.xvg Output xvgr/xmgr file -otwist twist.xvg Output xvgr/xmgr file -obendingbending.xvg Output xvgr/xmgr file -otilt tilt.xvg Output xvgr/xmgr file -orot rotation.xvg Output xvgr/xmgr file Option Type Value Description -- -[no]h bool yes Print help info and quit -[no]version bool no Print version info and quit -niceint19 Set the nicelevel -b time 0 First frame (ps) to read from trajectory -e time 0 Last frame (ps) to read from trajectory -dt time 0 Only use frame when t MOD dt = first time (ps) -xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none -[no]sidechain bool no Calculate sidechain directions relative to helix axis too. -[no]incremental bool no Calculate incremental rather than total rotation/tilt. This is not the content to which I was referring. There are input/output options. The last paragraph of the help description is as follows: The tilt/rotation is calculated from Euler rotations, where we define the helix axis as the local x-axis, the residues/Calpha vector as y, and the z-axis from their cross product. We use the Euler Y-Z-X rotation, meaning we first tilt the helix axis (1) around and (2) orthogonal to the residues vector, and finally apply the (3) rotation around it. For debugging or other purposes, we also write out the actual Euler rotation angles as theta[1-3].xvg I believe this answers your question. Some help descriptions are quite long and the information you need may pass by in the terminal. Everything contained in the help description for all tools is also printed in the manual. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Coordinate file for lipid bilayer
Dear all! Recently I've forced with the same problem as was in this topic :) I have tieleman's lipids consisted of 128 dppc with water. also I have system with the protein inserted in the same bilayer I wounder to know 1- How I could change lipid number in the pure lipid bilayer ( increase up to 200 lipids) with standard Gromacs tools ? I've tried use genbox -cs dppc128_whole.gro -box 8.04542 8.04542 10.19156 where 8.045 in x and y was higher than in the case of initial bilayer ( 6.045) As the consequence that prodyce larger system with increased amount of water in upper and lower layers but the lipid number was the same. 2- Is there any way to increase lipid number ( to add lipids from each size of the system) in the bilayer with the inserted protein ? Thanks for help, James 2012/6/11, Justin A. Lemkul jalem...@vt.edu: On 6/11/12 6:05 AM, James Starlight wrote: Dear all! Recently I've forced with the opposite problem. I have pre-equilbrated bilayer of highter dimensions than I need. How I could reduce lipid number of such bilayer as well as reduce total dimensions of such system ? E.g I have preequilibrated bilayer consisted of 340 lipids. I want to reduce it to the 200 lipids by the symmetrical deletion of the unnecessary lipids from each side. Is there simplest way to do it ? Try genbox with the -box option (with your bilayer as -cs) to set a smaller box size that will give a suitable number of lipids. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users 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] Coordinate file for lipid bilayer
On 10/2/12 2:16 PM, James Starlight wrote: Dear all! Recently I've forced with the same problem as was in this topic :) I have tieleman's lipids consisted of 128 dppc with water. also I have system with the protein inserted in the same bilayer I wounder to know 1- How I could change lipid number in the pure lipid bilayer ( increase up to 200 lipids) with standard Gromacs tools ? I've tried use genbox -cs dppc128_whole.gro -box 8.04542 8.04542 10.19156 where 8.045 in x and y was higher than in the case of initial bilayer ( 6.045) As the consequence that prodyce larger system with increased amount of water in upper and lower layers but the lipid number was the same. The proper approach is to set values for the box that are larger in x and y, but the same size in z. That way, the new solvation occurs within the same plane as the membrane. 2- Is there any way to increase lipid number ( to add lipids from each size of the system) in the bilayer with the inserted protein ? Using the same approach, with a slight modification: genbox -cp protein_in_membrane.gro -cs dppc128_whole.gro -box (x y z) Increase the values of x and y, and leave z alone. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] energy comparison
On 10/2/12 12:49 PM, Edward Deira wrote: Dear all, From the computational side of the question, can one compare the final energy values at the end of a simulation ? Are those energy values are meaningful ? Can I, with proper chemical judgement, say that a lower (more negative) value will correspond to a more stable system ? I will make several assumptions about what you're dealing with to try to answer this question. If I'm off-base, then please be (much) more specific about what you're doing. For a normal case of some solute in water, the potential energy is dominated by the water itself. The value of energy from a single snapshot really doesn't mean much, and the only comparison you might be able to make would be between identical systems, i.e. replicate simulations of the same starting configuration. If the systems differ at all in their contents, you're comparing apples and oranges since the potential energy is an extensive property. There are considerably more robust approaches to real free energy analysis coupled with conformational sampling that one can do. I would not be inclined to believe a stability argument based on a statement like the potential energy of snapshot A was lower than that of snapshot B, so therefore configuration A is more stable. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] energy comparison
not that off-base, actually. one of my aims is to compare two different proteins with the same ligand and try to figure out which system is energetically more favourable without having to go through qm/mm. so i suppose the proper way would be estimating the absolute free energy of the system. can i do that with gromacs ? i know that computing deltaG is ***trivial*** (not the best word,i know), but what about absolute values? On Oct 2, 2012 7:26 PM, Justin Lemkul jalem...@vt.edu wrote: On 10/2/12 12:49 PM, Edward Deira wrote: Dear all, From the computational side of the question, can one compare the final energy values at the end of a simulation ? Are those energy values are meaningful ? Can I, with proper chemical judgement, say that a lower (more negative) value will correspond to a more stable system ? I will make several assumptions about what you're dealing with to try to answer this question. If I'm off-base, then please be (much) more specific about what you're doing. For a normal case of some solute in water, the potential energy is dominated by the water itself. The value of energy from a single snapshot really doesn't mean much, and the only comparison you might be able to make would be between identical systems, i.e. replicate simulations of the same starting configuration. If the systems differ at all in their contents, you're comparing apples and oranges since the potential energy is an extensive property. There are considerably more robust approaches to real free energy analysis coupled with conformational sampling that one can do. I would not be inclined to believe a stability argument based on a statement like the potential energy of snapshot A was lower than that of snapshot B, so therefore configuration A is more stable. -Justin -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://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] Coordinate file for lipid bilayer
Justin, I've done exactly like you provide me ( changing only x and y ) but in that case the protein and the old lipids were slightly shifted to one side of the new system. Is there any way to center the old system in respect to the new solvent ? Also I've noticed that when I increase size of my system in x and y dimensions both of the water layers were increased greatly than lipid layer ( it's look like sandwich with two big bread pieces and smaller cutlet between them :) ) James 2012/10/2, Justin Lemkul jalem...@vt.edu: On 10/2/12 2:16 PM, James Starlight wrote: Dear all! Recently I've forced with the same problem as was in this topic :) I have tieleman's lipids consisted of 128 dppc with water. also I have system with the protein inserted in the same bilayer I wounder to know 1- How I could change lipid number in the pure lipid bilayer ( increase up to 200 lipids) with standard Gromacs tools ? I've tried use genbox -cs dppc128_whole.gro -box 8.04542 8.04542 10.19156 where 8.045 in x and y was higher than in the case of initial bilayer ( 6.045) As the consequence that prodyce larger system with increased amount of water in upper and lower layers but the lipid number was the same. The proper approach is to set values for the box that are larger in x and y, but the same size in z. That way, the new solvation occurs within the same plane as the membrane. 2- Is there any way to increase lipid number ( to add lipids from each size of the system) in the bilayer with the inserted protein ? Using the same approach, with a slight modification: genbox -cp protein_in_membrane.gro -cs dppc128_whole.gro -box (x y z) Increase the values of x and y, and leave z alone. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users 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] Coordinate file for lipid bilayer
On 10/2/12 2:56 PM, James Starlight wrote: Justin, I've done exactly like you provide me ( changing only x and y ) but in that case the protein and the old lipids were slightly shifted to one side of the new system. Is there any way to center the old system in respect to the new solvent ? Define a new box and center with editconf -c -box. Also I've noticed that when I increase size of my system in x and y dimensions both of the water layers were increased greatly than lipid layer ( it's look like sandwich with two big bread pieces and smaller cutlet between them :) ) This suggests that something is wrong with the z-dimension. I only say that because you had a 10-nm z-length in your previous post with the Tieleman DPPC bilayer, which is far larger than the coordinate file normally has. genbox works by tiling the solvent coordinates through the empty space in the solute configuration. If you're expanding in 3 dimensions, you can expect weird things to happen with membrane systems. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] energy comparison
On 10/2/12 2:45 PM, Edward Deira wrote: not that off-base, actually. one of my aims is to compare two different proteins with the same ligand and try to figure out which system is energetically more favourable without having to go through qm/mm. so i suppose the proper way would be estimating the absolute free energy of the system. can i do that with gromacs ? i know that computing deltaG is ***trivial*** (not the best word,i know), but what about absolute values? I have never attempted to calculate the absolute free energy of a given configuration, but again I suspect that you will fall victim to the same problems I have already described. Energy differences in these systems will be dominated by the solvent, which comprises somewhere between 75%-90% of the atoms in any system (unless it's implicit, of course). Small differences like different ligands (which may also induce protein conformational changes and thus differences in solute-solvent interactions, i.e. entropic changes in the solvent) will make your headaches worse. I suspect there's no trivial way to do this, as all of the quick-and-dirty approaches probably create more questions than they answer. Perhaps someone else who has actually attempted this can comment. I'm sure I've seen similar inquiries posted to the list before, so there may be something useful in the archive, as well. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Coordinate file for lipid bilayer
Justin Previously I've expanded initial system on Z-dim before the protein was inserted to increase both water layers. After current processing with Genbox there is no problems in Z actually- it look likes sandwich with two broader bread layers and narrower cutlet :) So the lipid layer in x and y is thinker than water ( so the lipid number stay the same after resizing). James 2012/10/2, Justin Lemkul jalem...@vt.edu: On 10/2/12 2:56 PM, James Starlight wrote: Justin, I've done exactly like you provide me ( changing only x and y ) but in that case the protein and the old lipids were slightly shifted to one side of the new system. Is there any way to center the old system in respect to the new solvent ? Define a new box and center with editconf -c -box. Also I've noticed that when I increase size of my system in x and y dimensions both of the water layers were increased greatly than lipid layer ( it's look like sandwich with two big bread pieces and smaller cutlet between them :) ) This suggests that something is wrong with the z-dimension. I only say that because you had a 10-nm z-length in your previous post with the Tieleman DPPC bilayer, which is far larger than the coordinate file normally has. genbox works by tiling the solvent coordinates through the empty space in the solute configuration. If you're expanding in 3 dimensions, you can expect weird things to happen with membrane systems. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users 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] Coordinate file for lipid bilayer
On 10/2/12 3:49 PM, James Starlight wrote: Justin Previously I've expanded initial system on Z-dim before the protein was inserted to increase both water layers. After current processing with Genbox there is no problems in Z actually- it look likes sandwich with two broader bread layers and narrower cutlet :) So the lipid layer in x and y is thinker than water ( so the lipid number stay the same after resizing). Posting a link to an actual image would be really useful here. I'm not sure I understand your metaphor exactly. If you're looking to add lipids and water around an existing system, the z-dimension of the solute and solvent boxes have to be the same. So if you have a system that you have extended in z to accommodate a protein or whatever else, you need to manipulate a DPPC-only system in the same way - extend its z-dimension to be the same as the solute, maintaining the relative position of the membrane within the new solvent box, and then add water in the solvent configuration to fill that box. Then proceed as I've suggested before. It should be obvious from all of this that it is vastly easier to plan a box of sufficient size before starting ;) -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Coordinate file for lipid bilayer
This is exactly what I've obtained http://imageshack.us/photo/my-images/27/89293914.png/ the same effect was also in case of intact tieleman's lipid bilayers ( the water layers were broader than lipid after resizing with genbox) James 2012/10/2, Justin Lemkul jalem...@vt.edu: On 10/2/12 3:49 PM, James Starlight wrote: Justin Previously I've expanded initial system on Z-dim before the protein was inserted to increase both water layers. After current processing with Genbox there is no problems in Z actually- it look likes sandwich with two broader bread layers and narrower cutlet :) So the lipid layer in x and y is thinker than water ( so the lipid number stay the same after resizing). Posting a link to an actual image would be really useful here. I'm not sure I understand your metaphor exactly. If you're looking to add lipids and water around an existing system, the z-dimension of the solute and solvent boxes have to be the same. So if you have a system that you have extended in z to accommodate a protein or whatever else, you need to manipulate a DPPC-only system in the same way - extend its z-dimension to be the same as the solute, maintaining the relative position of the membrane within the new solvent box, and then add water in the solvent configuration to fill that box. Then proceed as I've suggested before. It should be obvious from all of this that it is vastly easier to plan a box of sufficient size before starting ;) -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users 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] pull=constraint gives zero forces
Hi, I'm using the pull code to maintain the initial structure of a protein that otherwise deforms. Using pull=umbrella does what I expect it to, but pull=constraint produces zero forces. I'm using version 4.5.5 with the MARTINI force field. The pull=umbrella mdp contains the following, and gives the following pullf output: For such runs, the group COM:s stay within 0.1 nm of their initial positions, throughout a long trajectory. The pull=constraint mdp starts with and produces the pullf output For these runs, the group COM:s move around freely. I guess I'm doing something wrong but can't work out what. I've tried specifying k:s for the contraint runs, and tried removing all other constraints in the molecule. I've tried to comply with the manual's instructions but to no avail. Any ideas? Cheers, Alexander Björling, PhD candidate, University of Gothenburg, Sweden -- View this message in context: http://gromacs.5086.n6.nabble.com/pull-constraint-gives-zero-forces-tp5001538.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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: g_energy menu choices inconsistent?
Justin Lemkul wrote Note that you can always select by name rather than number, i.e.: echo Temperature | g_energy -f ener.edr That's undocumented, as of the GROMACS 4.5.4 manual, but VERY useful. Thanks. -- View this message in context: http://gromacs.5086.n6.nabble.com/g-energy-menu-choices-inconsistent-tp5001494p5001539.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] Coordinate file for lipid bilayer
On 10/2/12 4:12 PM, James Starlight wrote: This is exactly what I've obtained http://imageshack.us/photo/my-images/27/89293914.png/ This looks completely normal. What I was asking for was an image of one of your failed attempts that has whatever odd manifestation you've been trying to describe. the same effect was also in case of intact tieleman's lipid bilayers ( the water layers were broader than lipid after resizing with genbox) Sorry, I still don't understand. I've explained as clearly as I can how to proceed, if you need further help you will have to provide the exact commands you're using and why they're insufficient (again, pictures of failed systems, not normal ones, would help here). -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] xmgrace graphs
Dear Gromacs users, I am trying to find inter atomic distances between ligand atoms and protein residues using Gromacs commands and could generate individual xvg files, but could not figure out how to merge or show all the xvg files in one graph using xmgrace. Cold you please suggest? Thanks and Regards, Pramod -- 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] xmgrace graphs
Dear Pramod use the command xmgrace -nxy file1.xvg file2.xvg Instead of file1 and file2 use ur file name. On Tue, Oct 2, 2012 at 8:49 PM, ram bio rmbio...@gmail.com wrote: Dear Gromacs users, I am trying to find inter atomic distances between ligand atoms and protein residues using Gromacs commands and could generate individual xvg files, but could not figure out how to merge or show all the xvg files in one graph using xmgrace. Cold you please suggest? Thanks and Regards, Pramod -- 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 -- Regards N.NagaSundaram -- 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] Density measurment
Thank you Justin for your reply , I tried g_density again after your reply. But I found that it give density with respect to box dimension and not to time. g_densmap have xpm output and no the xvg ( I need density or no of water molecule present in between two peptides with respect to the time ).. Please, would you tell me another way to solve these problem..?? Thank you in advance Have a nice day. Rama David On Tue, Oct 2, 2012 at 8:28 PM, Justin Lemkul jalem...@vt.edu wrote: On 10/2/12 7:07 AM, rama david wrote: Hi Gromacs Users, I did simulation of two random coil peptides for 100ns. after 70 ns these peptide get converted to anti parallel beta sheet structure. I am interested to see the water density in between these peptideswith respect to time change and also the no of water molecule between the peptide with respect to time. And at the same time the distance between the peptide.. I need these information in xvg graph. I found out the distance between peptide by g_mindist but I not found the appropriate way to calculate density of water with respect to time between two peptides.. I used g_density but it not gave me the information as per my need. There are a variety of options in g_density that might work, like changing the direction along which the box is sliced, the interval of time examined, etc. I can envision this working quite well. g_densmap can do similar functions, and g_rdf can probably provide you with some useful information as well. -Justin -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://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] Re: gmx-users Digest, Vol 102, Issue 6
Hi. Thanks for the tip. I turned the problem was caused by the PDB file. It seems the water segment was not written properly (starting with residue 1 and then all the way to the last one). After correcting this and then manually editing the new PDB file to change the atom names from TIP3 to SPCE water (i.e. OH2 - OW ...), I was able to import the PDB to Gromacs. I also passed the option -renum to pdb2gmx so the atom numbering was corrected. Thanks for the tips! Regards, Jernej On Tue, Oct 2, 2012 at 3:54 PM, gmx-users-requ...@gromacs.org wrote: From: Peter C. Lai p...@uab.edu Subject: Re: [gmx-users] pdb2gmx with more than residues To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 20121002062613.gf94...@cesium.hyperfine.info Content-Type: text/plain; charset=us-ascii A pdb file with a resid exceeds the proper PDB format. You can resolvate a dry lipid bilayer using genbox fine; I don't know what problem you have with the solvation and minimization using that method, http://manual.gromacs.org/current/online/genbox.html You can also pdb2gmx or editconf the lipids and water separately as you suggested, then merge the files and run ediconf on the merged file to renumber the atoms. -- Windows: Re-Boot, Linux: Be-Root. -- 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] Coordinate file for lipid bilayer
Justin, I've told about lower lipid density at the left and right edges of the new system ( see new pic bellow with marked regions). http://imageshack.us/photo/my-images/10/dppc.png/ I've started with system consisted of 118 lipids and 6000 water in dims 6x6x10 I've created new box with the desired sizes for my system as well as centered it in it. Finally I've resized it via genbox -cp prot_in_lipids_old.gro -cs dppc128_whole.gro -box 8.04542 8.04542 10.19156 As the result I've obtain syste of 128 lipids and 13000 water with dims 8x8x10 I have the same system with the popc lipids with the same dims where there are 200 lipids Why only 10 lipids were added after resizing ? How I could increase this number of added lipids ( expesially in regions with lower lipid density- see pic) ? James 2012/10/2, Justin Lemkul jalem...@vt.edu: On 10/2/12 4:12 PM, James Starlight wrote: This is exactly what I've obtained http://imageshack.us/photo/my-images/27/89293914.png/ This looks completely normal. What I was asking for was an image of one of your failed attempts that has whatever odd manifestation you've been trying to describe. the same effect was also in case of intact tieleman's lipid bilayers ( the water layers were broader than lipid after resizing with genbox) Sorry, I still don't understand. I've explained as clearly as I can how to proceed, if you need further help you will have to provide the exact commands you're using and why they're insufficient (again, pictures of failed systems, not normal ones, would help here). -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users 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
