[gmx-users] do_dssp Segmentation fault

Hi all, I am meeting the following error in Gromacs 4.5.5 with do_dssp Here is the command do_dssp -f md.xtc -s md.tpr -o dssp.xpm give me the following error segmentation fault I have downloaded the executable DSSP form http://swift.cmbi.ru.nl/gv/dssp/ and set the environm

Re: [gmx-users] how to restart a stopped simulation

State_prev.cpt is the previous check point file to state.cpt. Usually the check point file generates for every 15 mins. You can use the state_prev.cpt because your state.cpt has no data (0 bytes) On Mon, Nov 12, 2012 at 11:54 AM, ananyachatterjee < ananyachatter...@iiserkol.ac.in> wrote: > Hi al

[gmx-users] Continuous mdrun vs step-by-step mdrun

Dear gromacs users, I have a very basic doubt regarding mdrun. Is there any difference between "doing final MD for 100 ns at a stretch" and "doing the same with a 10 ns step size (*i.e., 10ns20ns30ns100ns*) " on a cluster of 256 processors. I have read some where that continuous M

Re: [gmx-users] how to restart a stopped simulation

Hi all, I have restarted my simulation stopped due to power failure by using the command: mdrun -s md.tpr -cpi state.cpt -append And now I am getting the following error: Program mdrun, VERSION 4.0.7 Source code file: ../../../../src/gmxlib/checkpoint.c, line: 547 Fatal error: The checkpoi

Re: [gmx-users] how to restart a stopped simulation

Hi Ananya, You can refer this. http://www.gromacs.org/Documentation/How-tos/Doing_Restarts?highlight=restarting bye kavya On Mon, Nov 12, 2012 at 11:27 AM, ananyachatterjee < ananyachatter...@iiserkol.ac.in> wrote: > > Hi all, > > my simulation has stopped due to power failure, can anyone tell m

[gmx-users] how to restart a stopped simulation

Hi all, my simulation has stopped due to power failure, can anyone tell me how to restart it from the same point. -- Ananya Chatterjee, -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org

Re: [gmx-users] problem with MPI

FYI: If you are planning to run single-node, you don't need MPI. Just compile with default settings and you'll get a thread-parallel version that supports MPI parallelization within mdrun based on multi-threading (using the library thread-MPI). In practice his means that: $ mdrun -nt 2 will use two

Re: [gmx-users] problem with simulation of freezing of water

The phase transition of water from liquid to ice is very hard to observe in MD simulations. In the lab you can in fact supercool water for minutes without ice forming until you trigger the phase transition by e.g. knocking the beaker or add nucleating agents. An MD simulation takes place on time

[gmx-users] Re:problem with simulation of freezing of water

Hi, Also note that it is difficult to simulate the right structure of ice (Ih). You didn't write what you want to study, but search the literature carefully. You may need to use an ab-initio model. Ran Message: 7 Date: Sun, 11 Nov 2012 11:26:19 -0500 From: Justin Lemkul Subject: Re: [gmx-users]

Re: [gmx-users] Re:problem with simulation of freezing of water

On 2012-11-11 17:26, Justin Lemkul wrote: On 11/11/12 11:22 AM, Ali Alizadeh wrote: Dear Justin Thank you for reply, I want to simulation of water freezing, my condition: pressure=300 bar and T=240 k , number 1656, run time= 100ns, I can not see regular structure of ice by MD simulation or

Re: [gmx-users] Re:problem with simulation of freezing of water

On 11/11/12 11:22 AM, Ali Alizadeh wrote: Dear Justin Thank you for reply, I want to simulation of water freezing, my condition: pressure=300 bar and T=240 k , number 1656, run time= 100ns, I can not see regular structure of ice by MD simulation or by gromacs? In your opinion, if i want th

Re: [gmx-users] About periodic image of system.......

On 11/11/12 4:51 AM, rama david wrote: Hi justin , Thank you a lot for your explaination. My opinion on the working of g_mindist -pi is that when it shows the distance between two atom of the protein is less than vdw cut off ( 1.4 nm ) , then protein see it periodic image, and it is the viol

Re: [gmx-users] Re:Ka/Kd

On 11/11/12 7:47 AM, lloyd riggs wrote: Dear Justin, Thanks, Just a normal delta G then. I wondered if it also was doing a matrices from 2 columns if you supply something like just the 2d output from covar/anaeig (PCA). I did find a simple python 6 liner for just doing PCA with the first

Re: [gmx-users] problem with simulation of freezing of water

On 11/11/12 9:53 AM, Ali Alizadeh wrote: Dear All users I did simulation of water freezind at low temperature(260 k) so that i was hoped to see regular structure of ice, I used OPLS-AA force field, SPC and 100ns, But i can not see the regular structure of ice(i used vmd for representation o

Re: [gmx-users] Re:Ka/Kd

Dear Justin, Thanks, Just a normal delta G then. I wondered if it also was doing a matrices from 2 columns if you supply something like just the 2d output from covar/anaeig (PCA). I did find a simple python 6 liner for just doing PCA with the first (or any 2) derivatives just using numpy, and

Re: [gmx-users] About periodic image of system.......

Hi justin , Thank you a lot for your explaination. My opinion on the working of g_mindist -pi is that when it shows the distance between two atom of the protein is less than vdw cut off ( 1.4 nm ) , then protein see it periodic image, and it is the violation of pbc. Is these is right??? ( That i

Re: [gmx-users] constraining multiple types of bonds

thanks a lot Justin I'll try to follow this protocol. On Sun, Nov 11, 2012 at 8:59 AM, Justin Lemkul wrote: > > > On 11/10/12 10:27 PM, tarak karmakar wrote: >> >> Thanks Justin >> >> If I want to constrain all the bonds in the substrate molecule present >> inside the enzyme cavity then along wit