Re: [gmx-users] regarding charge group

Probably, make your broken molecules whole before passing them to grompp. Mark On Tue, Oct 22, 2013 at 8:26 AM, Sathish Kumar wrote: > The sum of the two largest charge group radii (13.336) is larger > than rlist(1.2) - rvdw/rcoulomb i am getting this error while running > membrane simulations.

[gmx-users] Minimum distance between periodic images

Dear all users I have simulated a protein with two chains (153 residues each) for 50ns(restarting crashed run 3 times) using a cubic box with each side as 11nm. After finding the closest distance between the periodic images, I found that the closest distance becomes lesser than 1 after 23ns for f

Re: [gmx-users] Minimum distance between periodic images

Hi Nidhi, These are periodicity artifacts. Make sure that you remove jumps over PBC from your trajectory by using trjconv -pbc nojump. Cheers, Tsjerk On Tue, Oct 22, 2013 at 11:14 AM, Nidhi Katyal wrote: > Dear all users > > I have simulated a protein with two chains (153 residues each) for >

[gmx-users] Regarding membrane(DMPC) simulations with fullerene

Dear Sir, I am doing fullerene interaction with DMPC , i downloaded the gro file from the website mentioned in the tutorial. I was keep the fullerene on the top of DMPC. But in the gro file already water is present. If i removed that water molecules and adding new water molecul

Re: [gmx-users] Minimum distance between periodic images

Thank you sir. On Tue, Oct 22, 2013 at 2:48 PM, Tsjerk Wassenaar wrote: > Hi Nidhi, > > These are periodicity artifacts. Make sure that you remove jumps over PBC > from your trajectory by using trjconv -pbc nojump. > > Cheers, > > Tsjerk > > > On Tue, Oct 22, 2013 at 11:14 AM, Nidhi Katyal >wr

[gmx-users] a new GROMACS simulation tool

Hi Everyone, I'm writing to let you guys know that we have developed a web-based tool MD simulation tool for GROMACS. It is a software package primarily developed for biological MD and offers a huge amount of possible options and settings for tailoring the simulations. Seamlessly integrated with

Re: [gmx-users] a new GROMACS simulation tool

Is there a link to the documentation? It's a little difficult to know exactly what this supposed to be doing. Is it a GUI interface to gromacs? In general, it would be great to get these sort of extensions coordinated with the main gromacs development tree, since otherwise they would tend to get

[gmx-users] Problems about the output force

Dear all, I have some doubt for the output force. What contributions do the output forces in .trr file include? Certainly, the pair forces and bonded interactions are included. However, if the external field (such as electric field) is applied, is the external force included? In addition, if the c

RE: [gmx-users] a new GROMACS simulation tool

Hi Michael, Sorry, if this is not the right place to post message of such. To answer your question, it is a web-based GUI interface to GROMACS, which is a perfect fit for those who are trying to learn MD or to run large scale protein simulations on HPC. Best Regards, Kevin"Feng" Chen, Ph.D. XSE

Re: [gmx-users] Regarding membrane(DMPC) simulations with fullerene

On 10/22/13 9:15 AM, Sathish Kumar wrote: Dear Sir, I am doing fullerene interaction with DMPC , i downloaded the gro file from the website mentioned in the tutorial. I was keep the fullerene on the top of DMPC. But in the gro file already water is present. If i removed th

[gmx-users] Conflicting atom names when using g_density

Hi Everyone, I am having an awkward situation. I want to use g_density to get the density profile of a lipid bilayer. At first glance, it looks like a trivial task. But for my case, it's not because I have conflicting atom names from two different molecules. I am using GROMOS 53a6. In DPPC topolog

Re: [gmx-users] Conflicting atom names when using g_density

On 10/22/13 9:05 PM, Bin Liu wrote: Hi Everyone, I am having an awkward situation. I want to use g_density to get the density profile of a lipid bilayer. At first glance, it looks like a trivial task. But for my case, it's not because I have conflicting atom names from two different molecules.

Re: [gmx-users] Re: [gmx-developers] v4.6.3: cmake-stage error at CMakeLists.txt:102

Hi! It is strange but such combination works: CC=icc CXX=icpc ~/cmake-2.8.12/bin/cmake .. -DCMAKE_INSTALL_PREFIX=/ifs/apps/GROMACS-4.6.3 -DGMX_X11=OFF -DGMX_MPI=ON -DGMX_FFT_LIBRARY=mkl -DGMX_GPU=ON >&cmake.log It was a command that our cluster administrator was able to configure GROMACS wi

[gmx-users] Energy minimizations taking really, really long?

I have some simulations of inserting a probe molecule into a bilayer. Some molecules work fine. However, a certain class of molecules is taking an absurdly long time to run the exact same simulation, even though I energy minimized the molecules individually beforehand and there are no overlaps.

[gmx-users] Box size increases in NPT

Hello, I am running a NPT simulation for cyclopropylchloride(1) in 50%water(100)+50%ethanol(100) using opls force field parameter . After equilibration box size increases from 20 A to 70 A. I used the following mdp file. ; RUN CONTROL PARAMETERS = integrator = sd ; start time and

[gmx-users] Re: Energy minimizations taking really, really long?

It depending the time steps that u used or the molecule that u had is big..Thats why ur EM take a long time..Is better take a long time rather than quick but had a lot of errors.. On Wed, Oct 23, 2013 at 9:59 AM, Nimmy McNimmerson [via GROMACS] wrote: > I have some simulations of inserting a prob

[gmx-users] Continuing runs from 4.5.4 in 4.6.3

Hi, We recently had a software upgrade in our cluster from gromacs 4.5.4. to gromacs 4.6.3.. I need to continue an earlier simulation that had been run in 4.5.4. using the .cpt, .tpr and .mdp. Are there any issues with continuing these runs in 4.6.3.? Can I concatenate these trajectories for late