[gmx-users] local pressure calcuation for Gromacs-4.5

Hi All, I found there is a customised version "gromacs-4.0.2_localpressure" for calculating the local pressure from the Gromacs website. I am wondering is there a higher version? The reason is that I am using CHARMM FF and have done membrane simulations using Gromacs-4.5. If I understand cor

[gmx-users] Re: QMMM with ORCA

Dear Gerrit, Thanks for your comments. Strange enough, once I set up the neighbour search from simple to grid, even the electronic embedding went through. But I'm not sure if the calculation is right. Generally, what happens if one is running a calculation without PBC but the calcul

[gmx-users] Re: QMMM with ORCA

Dear Xiaohu, Thanks for bringing this up. The comment has been there for ever. Since I could not think of an application where one would not be using pbc at the time. However, your clusters prove me wrong. In any case, as a work-around, you may want to use a bigger box, with long enough cut-of

[gmx-users] truncated LJ potential

Dear Mark and all: Dr. Mark Abraham wrote: > > and set the environment variable? > > You'd only have learned to do this if you'd used a debugger to step > through the flow of the code. I highly recommend that procedure. > init_forcerec() checks an environment variable and triggers the use of >

[gmx-users] Simulation time losses with REMD

Hi, I compared the .log file time accounting for same .tpr file run alone in serial or as part of an REMD simulation (with each replica on a single proessor). It ran about 5-10% slower in the latter. The effect was a bit larger when comparing the same .tpr on 8 processors with REMD with 8 pro

Re: [gmx-users] solvation_box_preparation

On 28/01/2011 3:51 PM, shahid nayeem wrote: Thanks Justin I tried with new box size of 2.8x2.8x2.8 . During energy minimization with steepest descent to force of 2000 and constraint=none, the system converged in 754 steps with positive potential energy. In subsequent simulated annealing with cons

Re: [gmx-users] truncated LJ potential

On 28/01/2011 3:44 PM, Makoto Yoneya wrote: Dear Mark and all: Dr. Mark Abraham wrote: So you have to update the machinery that parses the .top to recognise that the value of 4 is now legal. and also Did you set the environment variable to actually call the generic nonbonded lists? Thanks a

Re: [gmx-users] Eigenvectors

Hi Yao, They are. But if you really want to check, convert the eigenvectors to a human readable format (.gro/.g96) and calculate inner products :) Cheers, Tsjerk On Fri, Jan 28, 2011 at 2:43 AM, Yao Yao wrote: > > > >> Hi Gmxers, >> >> I am just wondering if the eigenvectors in gromacs are >>

Re: [gmx-users] solvation_box_preparation

Thanks Justin I tried with new box size of 2.8x2.8x2.8 . During energy minimization with steepest descent to force of 2000 and constraint=none, the system converged in 754 steps with positive potential energy. In subsequent simulated annealing with constraint all bonds it starts giving link warning

[gmx-users] truncated LJ potential

Dear Mark and all: Dr. Mark Abraham wrote: > So you have to update the machinery that parses the .top to recognise > that the value of 4 is now legal. and also > Did you set the environment variable to actually call the generic > nonbonded lists? Thanks a lot for your comments. I did not care t

[gmx-users] g_mindist clarification

Hi all !! Can some one clarify me what the g_mindist does. As far as I understood, it takes two inputs from the index file. If I have more than one entry in both of the indexes than how would g_mindist function? eg; echo "7 8" | g_mindist -s ../md30-60.tpr -n index.ndx -f ../30-60.part0004.trr

[gmx-users] nstcomm set to 10

Dear gmxusers, I have a question here concerning nstcomm. I got the note below after doing grompp, I'd like to do something about it. NOTE 1 [file HW_NPT.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting nstcomm to nstcalcenergy Currently, my nstcomm is

Re: [gmx-users] Output error mpirun/mdrun_mpi

Justin Kat wrote: Dear gmx-users, My colleague seems to be experiencing an output containing errors after issuing the command below: mpirun -np 8 mdrun_mpi -s *.tpr -o *.tpr -c out -v >& outt.mdrun_md The output reads as follows: NNODES=8, MYRANK=0, HOSTNAME=node3.reyclus.loc NODEID=0 a

[gmx-users] Output error mpirun/mdrun_mpi

Dear gmx-users, My colleague seems to be experiencing an output containing errors after issuing the command below: mpirun -np 8 mdrun_mpi -s *.tpr -o *.tpr -c out -v >& outt.mdrun_md The output reads as follows: NNODES=8, MYRANK=0, HOSTNAME=node3.reyclus.loc NODEID=0 argc=8

[gmx-users] Eigenvectors

> Hi Gmxers, > > I am just wondering if the eigenvectors in gromacs are > normalized or not. > thanks, > > Yao -- 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/Maili

Re: [gmx-users] Slow Runs

On Thu, 27 Jan 2011 19:17:18 -0500 Chris Neale wrote: > In addition, you're only updating your neighbourlist every 40 ps. Surely, this should be *femto*seconds. > If you're going to use a 4 fs timestep, I suggest that you use > nstlist=5. Also, you appear to not be using any constraints while y

[gmx-users] Slow Runs

In addition, you're only updating your neighbourlist every 40 ps. If you're going to use a 4 fs timestep, I suggest that you use nstlist=5. Also, you appear to not be using any constraints while you are using a 4 fs timestep. I suggest that you stop worrying about why the run is slower and do

Re: [gmx-users] truncated LJ potential

On 27/01/2011 12:11 PM, Makoto Yoneya wrote: Dear Berk and all: I'd tried to rewrite the routine src/gmxlib/nonbonded/nb_generic.c to modify the LJ potential to the shifted and truncated one. First, I'd add the new switch(ivdw) as case 4, but when I'd tried; [ defaults ] ; nbfunc comb-rule

Re: [gmx-users] Center of mass motion removal for partial filled PBC box

On 28/01/2011 4:25 AM, WU Yanbin wrote: Dear GMXers, I would like to reproduce the water droplet contact angle on graphite surface, as in Werder, T.; Walther, J. H.; Halicioglu, T.; Koumoutsakos, P. /J. Phys. Chem. B/ *2003*, /107/, 1345-1352. The box size is 20nm by 20nm by 30nm. Graphite i

Re: [gmx-users] Slow Runs

Denny Frost wrote: about 12000 atoms, 8 nodes, CentOS 5.3/Linux, infiniband. Below is a copy of my mdp file. title = BMIM+PF6 cpp = /lib/cpp constraints = all_bonds integrator = md dt = 0.004 ; ps ! nsteps =

Re: [gmx-users] Slow Runs

about 12000 atoms, 8 nodes, CentOS 5.3/Linux, infiniband. Below is a copy of my mdp file. title = BMIM+PF6 cpp = /lib/cpp constraints = all_bonds integrator = md dt = 0.004 ; ps ! nsteps = 2000 ; total 4ns.

RE: [gmx-users] Slow Runs

You will need to provide more details on the system. How many atoms, what sort of computer system is it being run on, how many nodes, copy of the mdp file etc. Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381

[gmx-users] Slow Runs

I am taking over a project for a graduate student who did MD using Gromacs 3.3.3. I now run similar simulations with Gromacs 4.5.1 and find that they run only about 1/2 to 1/3 as fast as the previous runs done in Gromacs 3.3.3. The runs have about the same number of atoms and both use opls force

[gmx-users] Eigenvectors

Hi Gmxers, I am just wondering if the eigenvectors in gromacs are normalized or not, and how to check that after the normal mode analysis/ thanks, Yao -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at h

[gmx-users] Eigenvectors

Hi Gmxers, I am just wondering if the eigenvectors in gromacs are normalized or not, and how to check that after the normal mode analysis/ thanks, Yao -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at h

Re: [gmx-users] remove all waters from the pdb file

Dear Tsjerk, Thank you. Problem is solved. Removing waters from the pdb file: grep -v "HOH" xxx.pdb > nosol.pdb 27 Ocak 2011 21:37 tarihinde Tsjerk Wassenaar yazdı: > Hey, > > Well, for those things it also doesn't hurt to know a few standard linux > tools: > > grep -v "SOL" xxx.pdb > nosol.

[gmx-users] QMMM with ORCA

Dear GMX code writters, Could anyone tell me why this comments in the code *mdlib/qmmm.c appear*?(version 4.5.3) at *line ~ 714*, in the beginning of subroutine* update_QMMMrec* == */* updates the coordinates of both QM atoms and MM atoms

Re: [gmx-users] remove all waters from the pdb file

Hey, Well, for those things it also doesn't hurt to know a few standard linux tools: grep -v "SOL" xxx.pdb > nosol.pdb And if there are also ions in play: grep -v "\(SOL\|NA\|CL\)" xxx.pdb > nosol.pdb Hope it helps, Tsjerk 2011/1/27 Justin A. Lemkul : > > > ahmet yıldırım wrote: >> >> Dear u

Re: [gmx-users] protein movement in lipid bilayer during simulation

Dear Justin, Thanks for the suggestion. Best, Ram On Thu, Jan 27, 2011 at 6:46 PM, Justin A. Lemkul wrote: > > > ram bio wrote: >> >> Dear Gromacs Users, >> >> I am performing an all-atom simulation of protein ligand complex in >> lipid bilayer , but after around 100ns, I see that the protein

Re: [gmx-users] protein movement in lipid bilayer during simulation

ram bio wrote: Dear Gromacs Users, I am performing an all-atom simulation of protein ligand complex in lipid bilayer , but after around 100ns, I see that the protein started moving in one dimension in the lipid bilayer that is it is not in the centre, I want the position of the protein fixed t

[gmx-users] Center of mass motion removal for partial filled PBC box

Dear GMXers, I would like to reproduce the water droplet contact angle on graphite surface, as in Werder, T.; Walther, J. H.; Halicioglu, T.; Koumoutsakos, P. *J. Phys. Chem. B* *2003*, *107*, 1345-1352. The box size is 20nm by 20nm by 30nm. Graphite is represented by a two-layer carbon sheet. Af

Re: [gmx-users] Using g_select to detect water pores in a bilayer

Hi On Thu, Jan 27, 2011 at 16:18, Manuel Nuno Melo wrote: > My idea is to count the number of water molecules within a certain z > distance of the bilayer center, and flag a pore above a certain threshold. > The problem is that the position of this z-slab cannot be hardcoded because > my simulati

[gmx-users] protein movement in lipid bilayer during simulation

Dear Gromacs Users, I am performing an all-atom simulation of protein ligand complex in lipid bilayer , but after around 100ns, I see that the protein started moving in one dimension in the lipid bilayer that is it is not in the centre, I want the position of the protein fixed through out the simu

Re: [gmx-users] QMMM with ORCA

Hi Xiaohu, We are using gromacs/ORCA quite a lot. It works like any of the other interfaced programs and whether you should use it depends on your needs to the QM part of the QM/MM calculation. I am using gromacs 4.0.7, but I downloaded the 4.5.3 version to test it. I could not reproduce you

[gmx-users] Using g_select to detect water pores in a bilayer

Hello, I have a coarse-grain lipid bilayer system with a pore-forming peptide. I am trying to use g_select to automate the detection of the opening of a water pore. My idea is to count the number of water molecules within a certain z distance of the bilayer center, and flag a pore above a certain

Re: [gmx-users] solvation_box_preparation

shahid nayeem wrote: Dear All I am sending this mail again on user list because my reply to Mark’s query was not uploaded on the list. Original messge: I am trying to prepare a solvation box of chaps. After generating .itp and .gro at ProDrg and thorough check of charges, I started with a bo

[gmx-users] solvation_box_preparation

Dear All I am sending this mail again on user list because my reply to Mark’s query was not uploaded on the list. Original messge: I am trying to prepare a solvation box of chaps. After generating .itp and .gro at ProDrg and thorough check of charges, I started with a box size of 6x6x6. Energy m

Re: [gmx-users] Re: change in the secondary structure after simulation

Hi Bharat, If you have used the -deffnm option then the output gro will be called whatever name you used for the -deffnm option and not the default confout.gro. Tom Justin A. Lemkul wrote: bharat gupta wrote: I didn't gave any -c flag while md run .. and there is no confout.gro in my fold

Re: [gmx-users] Re: change in the secondary structure after simulation

bharat gupta wrote: I didn't gave any -c flag while md run .. and there is no confout.gro in my folder .. I have attached the graph obtained after energy minimzation I've never heard of such a thing. mdrun produces several files automatically: traj.trr, ener.edr, md.log, and confout.gro.

Re: [gmx-users] Re: change in the secondary structure after simulation

> I didn't gave any -c flag while md run .. and there is no confout.gro in > my folder .. I have attached the graph obtained after energy minimzation .. > I want to ask why the graph is not coming like the one shown in the tutorial > .. I guess I asked that same question earlier also ?? .. Here i

Re: [gmx-users] remove all waters from the pdb file

ahmet yıldırım wrote: Dear users, I want to remove all waters from the xxx.pdb file. Then, I want to save the pdb file (new pdb) without waters because I will use the methanol as a solvent. I looked at mail list but I could not find the answer I wanted. What should I do? Please read trj

[gmx-users] remove all waters from the pdb file

Dear users, I want to remove all waters from the xxx.pdb file. Then, I want to save the pdb file (new pdb) without waters because I will use the methanol as a solvent. I looked at mail list but I could not find the answer I wanted. What should I do? Thanks in advance -- Ahmet YILDIRIM -- gmx-

Re: [gmx-users] Re: change in the secondary structure after simulation

bharat gupta wrote: I don't think that there is any problem in the structure .. since I am simulating the crystal structure taken from PDB ... and I have checked the structure generated after pdb2gmx and solvation.. Since I am reapeating the simulation again I want to know and I am on energ

Re: [gmx-users] Re: change in the secondary structure after simulation

I don't think that there is any problem in the structure .. since I am simulating the crystal structure taken from PDB ... and I have checked the structure generated after pdb2gmx and solvation.. Since I am reapeating the simulation again I want to know and I am on energy minimzation step I want t

Re: [gmx-users] proton proton exchange and constant pH simulations.

On 27-01-2011 11:29, Mark Abraham wrote: On 27/01/2011 9:44 PM, Olga Ivchenko wrote: Dear gromacs users, I want to ask if is it possible to amke proton proton exchange simulations by now and constant pH simulations in new versions of Gromacs. Not sure what you mean, but probably not. See recen

Re: [gmx-users] proton proton exchange and constant pH simulations.

Olga Ivchenko wrote: Just I heard that molecular mechanics proton proton transfer should be soon implemented in gromacs. That's why I am, asking it. When a new version is released, the new features will be announced. As of right now, these algorithms are under development and have not yet

Re: [gmx-users] proton proton exchange and constant pH simulations.

Just I heard that molecular mechanics proton proton transfer should be soon implemented in gromacs. That's why I am, asking it. 2011/1/27 Mark Abraham > On 27/01/2011 9:44 PM, Olga Ivchenko wrote: > >> Dear gromacs users, >> >> I want to ask if is it possible to amke proton proton exchange simul

Re: [gmx-users] Re: change in the secondary structure after simulation

On 27/01/2011 11:11 PM, bharat gupta wrote: I used the same .mdp files that are given in the lysozyme tutorial .. Since I was knowing what all parameters to change .. but after energy minimization and equilibration steps , the graphs that I got were fine ... even the rmsd graph of the final str

Re: [gmx-users] Re: change in the secondary structure after simulation

I used the same .mdp files that are given in the lysozyme tutorial .. Since I was knowing what all parameters to change .. but after energy minimization and equilibration steps , the graphs that I got were fine ... even the rmsd graph of the final structure is also fine .. I have attached the final

Re: [gmx-users] Re: change in the secondary structure after simulation

bharat gupta wrote: I generated the secondary structure profile of structure retrieved from the last frame of the simulation ... In that profile those amino acids that are shown as loops in VMD doesnot have any secondary structure assignment ... it means that during simulation the structure g

Re: [gmx-users] Re: change in the secondary structure after simulation

I generated the secondary structure profile of structure retrieved from the last frame of the simulation ... In that profile those amino acids that are shown as loops in VMD doesnot have any secondary structure assignment ... it means that during simulation the structure got changed some how ... an

Re: [gmx-users] gro to itp

trevor brown wrote: Dear all, I obtained a gro file with g_x2top for a CNT. I deleted [commands] in t and saved it as XXX.itp What is [commands]? Is it true? If no, how can I convert it into .itp? A .gro file contains coordinates, while an .itp file is a topology. They're not intercon

Re: [gmx-users] Re: change in the secondary structure after simulation

Mark Abraham wrote: On 01/27/11, *bharat gupta * wrote: I actually don't understand exactly what u are asking .. since I am not an expert with gromacs.. Please leave the old context for the discussion in future emails. Only you are paying so much attention to your work that you can be s

Re: [gmx-users] proton proton exchange and constant pH simulations.

On 27/01/2011 9:44 PM, Olga Ivchenko wrote: Dear gromacs users, I want to ask if is it possible to amke proton proton exchange simulations by now and constant pH simulations in new versions of Gromacs. Not sure what you mean, but probably not. See recent publications from Lindahl group for w

[gmx-users] proton proton exchange and constant pH simulations.

Dear gromacs users, I want to ask if is it possible to amke proton proton exchange simulations by now and constant pH simulations in new versions of Gromacs. best, Olga -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archiv

[gmx-users] gro to itp

Dear all, I obtained a gro file with g_x2top for a CNT. I deleted [commands] in t and saved it as XXX.itp Is it true? If no, how can I convert it into .itp? best, trevor -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archiv

Re: [gmx-users] Re: Gromacs + GPU: Problems running dppc example in ftp://ftp.gromacs.org/pub/benchmarks/gmxbench-3.0.tar.gz

Hi Camilo, On Jan 27, 2011, at 7:19 AM, Camilo Andrés Jimenez Cruz wrote: > Sorry, abrupt sending, > > the coulombtype is the same > > coulombtype = cut-off Is your cut-off actually 0.0 then? Carsten > > and constraints = all-bonds is the same. Any idea? > > 2011/1/27 Cami

Re: [gmx-users] ZN2+ qtot 1.233e-06 ?

On 27/01/2011 7:23 PM, Chih-Ying Lin wrote: Hi I issued "pdb2gmx with G45a3 force field" on the "bovine carbonic anhydrase" From the .top value, the ZN+2 is given qtot 1.233e-06 .. 2611 ZN2+257 ZN ZN 1137 2 65.37 ; qtot 1.233e-06 I am con

[gmx-users] ZN2+ qtot 1.233e-06 ?

Hi I issued "pdb2gmx with G45a3 force field" on the "bovine carbonic anhydrase" From the .top value, the ZN+2 is given qtot 1.233e-06 .. 2611 ZN2+257 ZN ZN 1137 2 65.37 ; qtot 1.233e-06 I am confused with the charges. Isn't ZN+2 carrying +2 cha

Re: [gmx-users] Re: change in the secondary structure after simulation

On 01/27/11, bharat gupta wrote: > I actually don't understand exactly what u are asking .. since I am not an > expert with gromacs..  > Please leave the old context for the discussion in future emails. Only you are paying so much attention to your work that you can be sure of remembering

Re: [gmx-users] ZN2+ qtot 1.233e-06 ?

On 01/27/11, Chih-Ying Lin wrote: > > > > > Hi > I issued "pdb2gmx with G45a3 force field" on the "bovine carbonic anhydrase"  > > > From the .top value, the ZN+2 is given qtot 1.233e-06 .. > > > >   2611       ZN2+    257     ZN     ZN   1137          2      65.37   ; qtot > 1.23