[gmx-users] Can we connect two boxes together for the simulation?

Hi, all, I want to do NPT simulations with different compositions first. Then I want to connect the two boxes to continue the NPT simulation. I mean, after simulations, we get two boxes with different compositions. Can we do that with gromacs? or how can we do that? Thanks. Best, Kai --

[gmx-users] Can we connect two boxes together for the simulation?

into another box using cat box1.gro box2.gro, just remove the very last line in box1.gro. Dr. Vitaly Chaban On Tue, Jun 4, 2013 at 2:46 PM, Bao Kai paeanball at gmail.com http://lists.gromacs.org/mailman/listinfo/gmx-users wrote: * Hi, all, I want to do NPT simulations with different

[gmx-users] On pressure controlling

Dear all, I am wondering if I can make the box only scale in one single direction, such as the z direction when controlling the pressure so that I can fix the area of the box in xy plane. I just want to fix the area of the interface during the NPT simulation. Thanks a lot. Best, Kai --

[gmx-users] Why the shape of the molecules changed?

Hi, all, I finally wrote a decane topology file. I used it to some simple simulation. The energy minimization works, while after a simple nvt equilibration, the shape of the molecules changed. Please find the images before and after the nvt equilibration from the following links.

[gmx-users] Why the shape of the molecules changed?

be different, right? Thanks, Kai On 5/23/13 11:16 AM, Bao Kai wrote: Hi, all, I finally wrote a decane topology file. I used it to some simple simulation. The energy minimization works, while after a simple nvt equilibration, the shape of the molecules changed. Please find the images

[gmx-users] On using CO2 as solvent

Hi, all, Following the tutorial on building biphasic system from Justin, I put the decane in a box and equilibrated it first. Then I increased the size of the box. Then I wanted to put some CO2 molecules to make a biphasic system. When I used the following command to do that, I can only add 16

[gmx-users] How to get the density change along one direction?

Hi, all, I performed some NPT simulations. I want to plot the density change, for one single time step or averaged over time, along some direction, such as x direction or y direction. I wonder how I can do that with the output files. It will be much better if it can be done separately for a

[gmx-users] On Decane coordinate file

to provide one .top or .itp file on decane. Generally any forcefield will work while OPLS-AA forcefield will be better. Thank you very much. Best Regards, Kai On 4/16/13 6:51 AM, Bao Kai wrote: Dear all, I am trying to do some two phase simulations with Decane molecules and some other smaller

[gmx-users] On Decane coordinate file

Hi, Rejesh, Thanks for the reply. Unfortunately, they does not have the topology file for decane. Best Regards, Kai virtualchemistry.org has some topology files for many organic liquids. Regards Rajesh On Tue, May 21, 2013 at 1:21 PM, Bao Kai paeanball at gmail.com wrote: Hi, Thank you

[gmx-users] How to visualize .gro file without .tpr file

HI, all, I have a small question here. I usually use ngmx to visualize the .gro or .trr file with a .tpr file. While after simulation, I use editconf to generate a new .gro file. Then I failed to visualize the new .gro file since the .tpr file did not work for the new .gro file now. I wonder

[gmx-users] On Decane coordinate file

Dear all, I am trying to do some two phase simulations with Decane molecules and some other smaller molecules. When I did simulations with smaller molecules, I specifies the properties based on each atom, while I just realized it is really not desirable to do it with Decane molecules ( 34 atoms

[gmx-users] On initialization of the molecules

Dear Gromacs Team and users, I have been using Gromacs for one of my projects before. For that project, I initialized the molecules in a random way. I mean, I used genbox to put the solute molecules (much fewer) first, then used genbox to put the solvent molecules (much more). Now, I want to

[gmx-users] The time for the temperature and pressure coupling

Dear Gromacs Team, I have a small question related to the scheme of the MD in Gromacs. When are the temperature and pressure constrains are enforced, before the update of the velocity and position or after? Thank you very much. Best Regards, Kai -- gmx-users mailing list

[gmx-users] How to avoid dumping trr file?

Hi, all, Sometimes I do not need to dump the .trr file, which is really big. I am wondering if I can avoid it? Thank you very much. Regards, Kai -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at

[gmx-users] The No. of the CO2 melecules in top file can not be updated correctly

file can not be updated correctly. To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 506e00de.9050...@vt.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed On 10/4/12 5:29 PM, Bao Kai wrote: Hi, all, I am still working on the molecular

[gmx-users] The No. of the CO2 melecules in top file can not be updated correctly.

Hi, all, I am still working on the molecular simulation of CO2 and H2O mixture. The information of the molecules types and the force field model are all defined in the a.top file. 1 [ defaults ] 2 ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ 3 1 3

[gmx-users] something wrong with BlueGene/P

Hi, all, I did many simulations with Gromacs on CO2 Water mixtures on my workstation with 8 cores in parallel, the results are pretty good. For bigger simulations, I turned to the BlueGene machine. The problem is that with exactly the same configuration files and same number of MPI tasks( 8

[gmx-users] What does --enable-fahcore mean?

Hi, all, I am wondering what the --enable-fahcore option of configure means. I got the explanation from configure --help of create a library with mdrun functionality, while it is not very clear to me. Best Regards, Kai -- gmx-users mailing listgmx-users@gromacs.org

[gmx-users] Can Gromacs functions be called by some other codes?

Hi, all, I am wondering if Gromacs functions can be called by some other codes. I know we get some library files and header files and we can write our own analysis tools. But I still wonder to what extent the gromacs can be coupled to other codes. For example, can we just generate the topology

[gmx-users] Re: Can Gromacs functions be called by some other codes?

, Kai From your description, why not just write a script to run various Gromacs programs (MD, analysis, etc)? dawei On Tue, Jun 12, 2012 at 2:43 PM, Bao Kai paeanball at gmail.com wrote: Hi, all, I am wondering if Gromacs functions can be called by some other codes. I know we get some

[gmx-users] Cannot get correct pressure value with MTTK pressure coupling

HI, all, I want to use MTTK for the pressure coupling for NPT simulation, while I can not get the correct pressure value. The following result is a simulation with 1000 SPC-E water molecules with temperature 303.15K and pressure 1 bar. Statistics over 101 steps [ 0. through 1000. ps

[gmx-users] How could I know whether I should use epsilon-sigma or c6-c12?

Hi, all, I am still trying to do my simulation with liquid mixtures. I have a simple question now. When I writing my .top file, how could I know if I should use epsilon-sigma or c6-c12 parameters for the LJ potential? It seems that in some examples, c6-c12 parameters are used and epsilon-sigma

[gmx-users] How could I know whether I should use epsilon-sigma or c6-c12?

. Thank you. Kai On 5/06/2012 4:34 PM, Bao Kai wrote: Hi, all, I am still trying to do my simulation with liquid mixtures. I have a simple question now. When I writing my .top file, how could I know if I should use epsilon-sigma or c6-c12 parameters for the LJ potential? It seems that in some

[gmx-users] What does this message mean?

Hi, all, It is very easy for me to get the following message. WARNING: nmol = 1, this may not be what you want. Temperature dependent fluctuation properties at T = 317.98. I am wondering if somebody can tell me what does it mean or if it is a problem to improve? Thank you very much. Best

[gmx-users] Re:What does this message mean?

--- gcq#74: Baseball Heroes Only (P.J. Harvey) Thank you. Kai On 5/06/2012 10:51 PM, Bao Kai wrote: Hi, all, It is very easy for me to get the following message. WARNING: nmol = 1, this may not be what you want. Temperature dependent fluctuation properties at T = 317.98. I am

[gmx-users] How to generate the initial coordinates file?

Hi, all, I am new to Gromacs and MD. I just went through a few tutorials on Gromacs quickly. I have a question now. I know the structure of molecule A and B, such as the atoms compositions and the relative position of the atoms and the charge. Now, I want to use 500 A and 100 B to do the

[gmx-users] Re: How to generate the initial coordinates file?

On 5/29/12 8:46 AM, Bao Kai wrote: Hi,  all, I am new to Gromacs and MD.  I just went through a few tutorials on Gromacs quickly.  I have a question now. I know the structure of molecule A and B, such as the atoms compositions and the relative position of the atoms and the charge. Now