[gmx-users] Time step problem on coarse-grained LJ chain
Dear all I am trying to simulate a Lennard-Jones coarse-grained polymer melt. Until know I simulated only one chain, in order to check if the parameters I used are OK. I simulated one chain of 50 LJ particles with *ε=1KJ/mol, m=1gr/mol, σ=1nm*. This means that my characteristic time of the system *τ=σ(m/ε)1/2* is *τ=1ps. * I am using RIGID bonds between the particles also with length *σ=1nm*. I have seen in many papers which are using similar systems that the time step they use is Dt=0.01τ. When I use *Dt=0.01τ* I don't get any error messages in my *.log* file or in the resulting *.gro* file. The problem that I have is when I am trying to convert my *.xtc* file to * .pdb* in order to visualize it in VMD. When I use: *trjconv -f ***.xtc -s ***.tpr -o ***.pdb -pbc whole* the trajectory looks fine. BUT, when I use *trjconv-f ***.xtc-s ***.tpr -o ***.pdb -pbc nojump* , it seems the chain is blowing after few steps (the bonds break and the particles spread in every direction). I would think that for a single chain, these two options of trjconv should not make such a difference. I used a relatively big box for the simulation (10 X 10 X 60). The *strange*think is that I don't have this problem when I increase the box size (to 50X50X60) , or of course when I decrease the time step. Is it possible that I am not able to use such a large time-step in GROMACS, or is it something with the *trjconv* that I don't understand ? Thanks in advance Best Regards, Chrysostomos -- 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] Problem when running in many nodes
Dear all The last days I switched from Gromacs 3.3.3 to Gromacs 4.5.3, but I experience some difficulties when running in parallel. Initially, my simulation box has dimensions : * 3.30507 2.67145 41.15800* and it consists of 25 polymers chains with 50 beads/chain When I run NVT using 8 or 16 cores, everything is working fine, but when I compress it to dimensions: *3.30507 2.67145 10.64441* and try again to run NVT in 8 cores, I have the following error message: *There is no domain decomposition for 8 nodes that is compatible with the given box and a minimum cell size of 2.5 nm Change the number of nodes or mdrun option -rcon or -dds or your LINCS settings* As I saw this is well known error, but I can't understand how to fix it :-) From what I understood, this is happening because* I use constrains in all the bonds of my system* In my .log file I see the following: *Initializing Domain Decomposition on 8 nodes Dynamic load balancing: auto Will sort the charge groups at every domain (re)decomposition Minimum cell size due to bonded interactions: 0.000 nm Maximum distance for 5 constraints, at 120 deg. angles, all-trans: 2.000 nm Estimated maximum distance required for P-LINCS: 2.000 nm This distance will limit the DD cell size, you can override this with -rcon Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25 Optimizing the DD grid for 8 cells with a minimum initial size of 2.500 nm The maximum allowed number of cells is: X 1 Y 1 Z 4* , but I can't understand how to use -rcon or -dds in order to fix my problem Any suggestions? Thanks in advance Chrysostomos -- 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] Reduced Units
Dear all I would like to do coarse-grained simulations using reduced LJ units. As I can see in the manual, this is possible, but I don't understand how... I use the Gromos96 53a6 force field. In the *ffG53a6nb.itp *the* σ* and *ε* are in *(nm*) and *(KJ/mol*) Also in the *ffG53a6.atp* the *mas*s is in* gr/mol*. Finally in the *mdp*file the *ref_t* is in *(K)* and the *time_step* in *(ps)* If I creat an atom A, and define *ε=σ=m=1*, how can I define that I want these numbers to be in reduced units? Also, how can I have reduced units in my *.mdp *file? Kind Regards, Chrysostomos -- 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] Problem with COM movement
Dear all I have the following system: Two substrates (which are FCC lattices consisting of LJ particles) in a distance of 50nm and between these substrates I put completely stretched polymer chains. The substrates are parallel to xy plane and the chains are vertical. The length of the stretched chains is 30 nm and I put them in the middle, so the distance of the each substrate to be 10nm. The interaction between the substrates and the polymers is repulsive and it’s the same for each substrate. I want my substrates to be stable during the simulation, but to be able also to move under compression (in the z axis). For that purpose in my .mdp file I define the following: *nstcomm = 1* *comm-grps= ZZZ **,where ZZZ is the name of the residue of the substrates* * * I have 2 problems: 1) At the beginning, I run NVT for 20ns and the chains are moving UP during the simulation. Since my system is completely symmetric, I would expect to have symmetric movement of the chains, i.e. symmetric density profile. 2) In my .log file the following message appears: *Large VCM(group rest): 0.0, -0.0, 0.1, T-cm: inf* It doesn’t appear as an error message, but it appears thousand times in my log file. I had a look in the mailing list about that, but I did not find a proper answer. Can anyone help me? I also have one question: When I remove that COM motion of one residue, i.e. from the ZZZ (by adding comm grps: ZZZ in my mdp file), what happening with the COM motion of the rest of the system? I hope I was clear! Thanks in advance, Chrysostomos -- 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] How to define Center of Mass velocity of a specific group
On Tue, Dec 14, 2010 at 2:19 PM, Justin A. Lemkul jalem...@vt.edu wrote: Tomy van Batis wrote: Dear all I have a system consisting of 2 substrates (20 nm distance between them) and inside them there are polymer chains. I would like during my NVT simulations the substrates NOT to move (I suppose I have to put the velocity of the COM of it's substrate to be zero). Does anyone know how to do that? The simplest way is to just use position restraints. The positions may change very slightly, but not a noticeable amount. If you absolutely require no movement at all, use freezegrps in the .mdp file. -Justin Thanks in advance Chrysostomos http://www.gromacs.org/Support/Mailing_Lists Dear Justin I found how to freeze the group that I want, but what I can't find is how to use the position restrains. I created just 1 chain. As I can see in my* topol.top* file it's automatically included the *posre.itp* file. I inserted in my *.mdp* file the following line: define = -DPOSRE but after running NVT for few steps I see that the chain is still moving a lot. I can't find any example in the manual or in the internet. Can you please tell me what to do? Many thanks Chrysostomos -- 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] How to define Center of Mass velocity of a specific group
Dear all I have a system consisting of 2 substrates (20 nm distance between them) and inside them there are polymer chains. I would like during my NVT simulations the substrates NOT to move (I suppose I have to put the velocity of the COM of it's substrate to be zero). Does anyone know how to do that? Thanks in advance Chrysostomos -- 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
