[gmx-users] Water droplet moving away from surface
Dear all, I am running an equilibration calculation using a new force field (GRAPPA), for a 10,000 water molecules on graphene. The run is up to 378 ps now. I am concerned that the water droplet will drift away from the surface, rather than forming a nice droplet.Is the cutoff values in my equilibration setup appropriate for this water/graphene in vacuum?I have shared the link to the XTC, PDB, and MDP files for my run.https://drive.google.com/file/d/0B7ym8d6G9-e2eUJQMDFLTlBBZ1U/edit?usp=sharingRegards,Kester -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] g_select syntax
Hi Everyone, I am recently puzzled by the syntax and behaviour of g_select. I want to obtain the residue index list of LIPID whose center of mass is within 1.0 nm of the surface of protein. In my case, each LIPID molecule consists of only one residue. I wrote the selection.dat as follows, and set -selrpos to atom and -seltype to res_com. Here I think "Protein" is the reference group, so -selrpos should be atom because I care about the distance to its surface. "LIPID" is the analysis group and I care about their individual center of mass. So -seltype should be res_com. selection.dat: resname LIPID and within 1.0 of group "Protein"; g_select -sf selection.dat -f traj.trr -s traj.tpr -n system.ndx -oi index.dat -seltype res_com -selrpos atom However I tried another selection. This time instead of retrieving the residue index, I tried to retrieve the index of a key atom of the LIPID molecule. selection.dat: rdist = res_com within 1.0 of group "Protein"; group_C15 = (resname LIPID) and (rdist) and (name C15); group_C15; g_select -sf selection.dat -f traj.trr -s traj.tpr -n system.ndx -oi index.dat -seltype atom -selrpos atom I thought these two selections should give the same number of indices per frame, as the second selection merely retrieve the atom indices of the corresponding key atoms in the LIPID molecules selected by the first selection. However the first selection gives significantly more indices than the second selection does. I guess my understanding of g_select syntax might be flawed. Please point out my misunderstanding. Thank you very much. Best Regards, Bin -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Martini force field for inhibitors
Dear Gromacs users, I have very recently started working with Gromacs and Martini force field. I am able to generate the coarse-grained model for HIV Protease (1hvr.pdb). I want to simulate the protein along with its inhibitor. Are there any guidelines for building (coarse-graining) its inhibitor ? Sorry for the naive question ... Thank you. -- Cheers !!! Sridhar Kumar Kannam :) -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] GPU Acceleration in case of Implicit Solvent Simulations
Dear all, Can we use periodic boundary conditions in case of implicit solvent simulations? If so, why? Also, can implicit solvent model in gromacs in any version (till 5.0) be implemented in more than 2 processors or can it at least use GPU acceleration provided by gromacs? I have tried using pbc=no and group cut-off scheme in gpu based gromacs V5.0, but there is a warning which says GPU is disabled because it effectively works only with verlet cut-off scheme and verlet cut-off scheme requires pbc=xyz or xy. Also tried implementing in gromacs version 4.5.5 using openMM after following the installation instructions in the following link, ( http://www.gromacs.org/Documentation/Installation_Instructions_4.5/GROMACS-OpenMM) and here again there is no luck as we dont have the compatible hardware. Thanks, Siva -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Positive Potential Energy.
Hey Daniel :) This doesn’t make sense as the molecule should fly apart with always > positive PE. > > You need a force to make things fly apart, but the force has little to do with the absolute PE. It's the gradients that do it. And as Justin points out, your system can choose between positive PE and even more positive PE. Cheers, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Positive Potential Energy.
On 8/28/14, 2:04 PM, Dan Sponseller wrote: Hello everyone. I am still fairly new to gromcs but I have researched this well. I am getting a positive potential energy (my bond energy is always positive) no matter how long I run my simulation. I also get this when doing minimizations. Even just one molecule set at know minimum conformation. Bond energy can only ever be zero (all bonds at exactly equilibrium values) or positive (not equilibrium values). I am running in vacuo with no pbc. I have read on the mail list that in vacuo can produce this? This doesn’t make sense as the molecule should fly apart with always positive PE. I have tried gromos ff and opsla ff. Both do this. A colleague of mine also gets this with his simulations although he reports negative potential when solvated. Negative potentials in condensed phase systems occur because of the massive amount of favorable nonbonded interactions, particularly hydrogen bonding between waters and with solute. Any help would be appreciated or any explanation on how to interpret gromacs output on this. I would question gromacs’ abilities if it cannot give a reasonable potential energy for a simple system. What is the system? Positive energy is indeed reasonable in vacuo. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Surface tension for membrane simulation
Hi all, I have a question of surface tension in membrane simulation. I found that in equilibration and production step, the pressure set up for membrane simulation is below: ; Pressure coupling is on pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT pcoupltype = semiisotropic ; uniform scaling of x-y box vectors, independent z tau_p = 2.0 ; time constant, in ps ref_p = 1.0 1.0 ; reference pressure, x-y, z (in bar) compressibility = 4.5e-5 4.5e-5 ; isothermal compressibility, bar^-1 I would like to know, during these steps, do we have constant pressure or constant surface tension? Moreover, different membrane have different surface tension, do we need to change and write it in the mdp file (ref_p value?) to run the simulation? Thanks a lot for your assistance! Best, Ning -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Positive Potential Energy.
Hello everyone. I am still fairly new to gromcs but I have researched this well. I am getting a positive potential energy (my bond energy is always positive) no matter how long I run my simulation. I also get this when doing minimizations. Even just one molecule set at know minimum conformation. I am running in vacuo with no pbc. I have read on the mail list that in vacuo can produce this? This doesn’t make sense as the molecule should fly apart with always positive PE. I have tried gromos ff and opsla ff. Both do this. A colleague of mine also gets this with his simulations although he reports negative potential when solvated. Any help would be appreciated or any explanation on how to interpret gromacs output on this. I would question gromacs’ abilities if it cannot give a reasonable potential energy for a simple system. Daniel Sponseller PhD student George Mason University -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] GB parameters for DNA
Dear everyone, I would like to simulate a DNA-protein complex using implicit solvent model. Anyone has the GB parameters for phosphorus atom? I searched the mailing list, but did not find the answer. Thanks in advance Cheers, Jianguo -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Cannot find "gmx_mpi" when installing gromacs 5.0
Dear Mark, Thank you for your response. But I can install gromacs 4.6.5 successfully with the same permission. I will still contact the administrator of the cluster. Do you have idea what permissions I should ask them for if I need to install 5.0? Any files or directories, or any permissions to execute files? I don't think it is good for gromacs installation to access some parts needing higher permissions. After all, most of users who need to install gromacs onto cluster are not administrators. Best, Jason >Date: Thu, 28 Aug 2014 08:45:40 +0200 >From: Mark Abraham >To: Discussion list for GROMACS users >Subject: Re: [gmx-users] Cannot find "gmx_mpi" when installing gromacs 5.0 >Message-ID: >Content-Type: text/plain; charset=UTF-8 >I'd guess your permissions on some part of >/users/yli/gromacs-5.0/exec/bin/gmx_mpi >are such that you can't access. >Mark On Thu, Aug 28, 2014 at 4:06 AM, ??? wrote: > Dear all, > > I am trying to install gromacs 5.0 by cmake on my cluster. But an error > occurs when I "make install". > > The "module list" for environment is given as below: > mvapich2/2.0rc1-intel > cmake/2.8.12.2 > intel/2013.1.106 > fftw/3.3.2 > > And the sequence of commands to execute is: > --- > cmake ../ \ > -DCMAKE_C_COMPILER=mpicc \ > -DCMAKE_CXX_COMPILER=mpicxx \ > -DGMX_X11=OFF \ > -DGMX_MPI=ON \ > -DCMAKE_INSTALL_PREFIX=/users/yli/gromacs-5.0/exec \ > -DCMAKE_INCLUDE_PATH=/gpfs/runtime/opt/fftw/3.3.2/include \ > -DCMAKE_LIBRARY_PATH=/gpfs/runtime/opt/fftw/3.3.2/lib/libfftw3f.a > > make > > make install > --- > > Configuration and "make" finished successfully. There are no errors or > warnings on the first two steps. However, an error shows up at the final > step of "make install" as below: > --- > .. > -- Up-to-date: > > /users/yli/gromacs-5.0/exec/include/gromacs/trajectoryanalysis/ analysismodule.h > -- Up-to-date: > > /users/yli/gromacs-5.0/exec/include/gromacs/trajectoryanalysis/ analysissettings.h > -- Up-to-date: > > /users/yli/gromacs-5.0/exec/include/gromacs/trajectoryanalysis/ cmdlinerunner.h > CMake Error at src/programs/cmake_install.cmake:42 (FILE): > file INSTALL cannot find "/users/yli/gromacs-5.0/exec/bin/gmx_mpi". > Call Stack (most recent call first): > src/cmake_install.cmake:40 (INCLUDE) > cmake_install.cmake:49 (INCLUDE) > > > make: *** [install] Error 1 > --- > > And the executable file "gmx_mpi" cannot be found anywhere. It is the first > time I install the version 5.0. The same installation and environments work > for the version 4.6.5. I am wondering if anyone has the same problems when > installing gromacs 5.0. I would appreciate it if you have any suggestion to > my installation. > > Thank you very much. > > Best, > Jason -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] MD exit condition
On Thu, Aug 28, 2014 at 3:32 PM, Eric Smoll wrote: > Hello Gromacs users, > > I am using Gromacs 4.6.5 > > Is there a way to set an exit condition during a simulation? I am > interested in terminating dynamics when two groups are separated by a > certain distance. > No. People want this, but it's never been a priority for someone with the knowledge to implement it. Creative use of a bond with a "malware" user table could produce infinite forces that will get mdrun to blow up shortly after the condition is reached, but I can't honestly recommend that! :-D One reasonable approach might be to use the pull code to achieve the distance in a controlled way. If it is not possible to set an exit condition, I suspect I can post > process the trajectory with trjconv using the -exec flag and/or the -trunc > flag: > > 1.) The manual states that the -exec flag will "Execute a command for every > output frame with the frame number as argument." What kinds of commands I > can pass to this flag? > Intended for use with -sep or -split. Command gets passed the number of the file most recently written, and then has to go do its own file parsing. I would rather use g_dist or such. 2.) If the "-exec" is not useful, I plan to analyse the the output of > g_dist to find the the time "t" when two groups exceed my distance > criterion and run "trjconv -trunc t" to crop the trajectory appropriately. > Is there a better way? > You could probably use NAMD :-) Mark > Best, > Eric > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] MD exit condition
Hello Gromacs users, I am using Gromacs 4.6.5 Is there a way to set an exit condition during a simulation? I am interested in terminating dynamics when two groups are separated by a certain distance. If it is not possible to set an exit condition, I suspect I can post process the trajectory with trjconv using the -exec flag and/or the -trunc flag: 1.) The manual states that the -exec flag will "Execute a command for every output frame with the frame number as argument." What kinds of commands I can pass to this flag? 2.) If the "-exec" is not useful, I plan to analyse the the output of g_dist to find the the time "t" when two groups exceed my distance criterion and run "trjconv -trunc t" to crop the trajectory appropriately. Is there a better way? Best, Eric -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Time varying electric field - phase term
Or, can you wait a while before you turn on the field? So far, I know that people can do npt after nvt. Can you run simulation without field, then, with field? Just have to count the delays. There might be some truncation effect tough if you turn on the field suddenly. On Wed, Aug 27, 2014 at 3:25 PM, steven shawn wrote: > Thanks for your reply Johnny Lu. That is a very good point. But I have not > seen any sin Electric field. Can gromacs generate sin Electric fields too? > > > On Tue, Aug 26, 2014 at 8:33 PM, Johnny Lu wrote: > > > I wonder if gromacs can do both sine and cosine? > > > > If so, the sum angle formula can work. > > > > > > > http://en.wikipedia.org/wiki/List_of_trigonometric_identities#Angle_sum_and_difference_identities > > > > > > > > On Sat, Aug 23, 2014 at 10:42 AM, steven shawn > > wrote: > > > > > Dear gromacs users, I am trying to use an electric field which is > varying > > > with time. I read the previous posts and successfully generated time > > > varying electric field with E-xt, E-yt and E-zt. > > > > > > but I need an electric field which has an initial phase term (ie. of > the > > > form E= E0cos(2*pi*f*t+some angle term)) where i want to specify the > > angle > > > term. Most of the posts i read mentioned this angle term must be > > specified > > > in the third term after E-xt. > > > I tried it but failed to generate an initial phase. Can anyone help me > > with > > > this? > > > > > > > > > thanks in advance. > > > -- > > > Gromacs Users mailing list > > > > > > * Please search the archive at > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > > posting! > > > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > * For (un)subscribe requests visit > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > > send a mail to gmx-users-requ...@gromacs.org. > > > > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] md simulation steps
Thank you. On Aug 28, 2014 11:04 AM, "Meenakshi Rajput" wrote: > hello > Can you tell me how many steps are sufficient for md simulation of > protein-ligand complex? > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] hydrogen bond correlation function
Dear all, I am doing a layerwise hydrogen bond lifetime correlation function (HBCF) for lysozyme-water system. I use "trjorder", "-r" to select the water within some distance (5 A) to the protein, and "-o" to generate a new trajectory. However, when g_hbond the trajectory, the HBCF shows very small (10e-4) values, which is certainly not true compared to HBCF between the protein and all water molecules. I wonder what is a correct way to select water near protein for further analysis. Many thanks, Yao -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] water not getting settle
Depends what the problem really is. See strategies at http://www.gromacs.org/Documentation/Terminology/Blowing_Up Mark On Thu, Aug 28, 2014 at 9:35 AM, Lovika Moudgil wrote: > Hi everyone , > > I am getting an error about water i.e > > step 168: Water molecule starting at atom 5226 can not be settled. > Check for bad contacts and/or reduce the timestep if appropriate. > > I have already tried reducing timestep ..but it didn't worked . If I freeze > water things work fine . But what if I do not want to freeze it !! What is > the other way to get it settled ? > > Thanks and Regards > Lovika > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] water not getting settle
Hi everyone , I am getting an error about water i.e step 168: Water molecule starting at atom 5226 can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. I have already tried reducing timestep ..but it didn't worked . If I freeze water things work fine . But what if I do not want to freeze it !! What is the other way to get it settled ? Thanks and Regards Lovika -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
