[gmx-users] Pulling and g_wham - Two analysis problems

Dear Gromacs users, I encountered two problems in using g_wham to calculate pmf curves from a pulling simulation. My system consists of a water molecule which is pulled through a bilayer (the reference group). I used gromacs 4.5.6 with the following pull code options: pull= umbrell

[gmx-users] Re: About Usage of restraint

Please post all Gromacs-related questions to gmx-users. On 2/8/13 8:46 AM, vidhya sankar wrote: Dear Justin Thank you for your previous Mail Reply As you Instructed me in the Previous Mail to insert Vertical Restraint I Have incr

[gmx-users] About Usage of Restraint

Dear Justin Thank you for your previous Mail Reply      As you Instructed me in the Previous Mail  to insert Vertical Restraint I Have increased  Value o

Re: [gmx-users] g_membed deprecated?

On Wed, Feb 6, 2013 at 6:01 PM, Albert wrote: > On 02/06/2013 05:37 PM, Namita Dube wrote: > >> Hi, >> There must be some kind of problem with your system. >> have you tried using : >> mdrun -s input.tpr -membed membed.dat -o traj.trr -c membed.pdb -e >> ener.edr >> -nt 1 -cpt -1 -mn index.ndx -m

Re: [gmx-users] compiling on different architecture than the compute nodes architecture

On Thu, Feb 7, 2013 at 10:00 AM, Broadbent, Richard < richard.broadben...@imperial.ac.uk> wrote: > Dear Silard, > > cmake -DGMX_CPU_ACCELERATION=AVX_256 -DGMX_DEFAULT_SUFFIX=OFF > -DGMX_BINARY_SUFFIX="_avx" -DGMX_OPENMP=ON -DGMX_MPI=ON -DGMX_DOUBLE=ON > -DGMX_GPU=OFF -DGMX_PREFER_STATIC_LIBS=ON

Re: [gmx-users] Reg:1 particles communicated to PME node 0 are more than 2/3 times the cut-off

On Fri, Feb 8, 2013 at 7:48 AM, Subramaniam Boopathi wrote: > dear sir, >how can i remove this following problem > >Energies (kJ/mol) > AngleProper Dih. Improper Dih. LJ-14 Coulomb-14 > 2.36059e+033.53976e+027.34586e+007.00084e+032.

Re: [gmx-users] Reg:1 particles communicated to PME node 0 are more than 2/3 times the cut-off

Doesn't that mean the npt should be done for a longer time? Sincerely, Shima From: Mark Abraham To: Discussion list for GROMACS users Sent: Friday, February 8, 2013 5:37 PM Subject: Re: [gmx-users] Reg:1 particles communicated to PME node 0 are more than 2

[gmx-users] Re: Membrane simulation - error during EM after inflation step

Hello Justin, I fixed the problem by placing my protein in its right position within the unit cell. Thank you so much for your timely help. John K -- View this message in context: http://gromacs.5086.n6.nabble.com/Membrane-simulation-error-during-EM-after-inflation-step-tp5005177p5005342.html

Re: [gmx-users] problems for GPU simulations

Hi: thanks for kind comments. It works fine now after I recompiled Gromacs carefully. best Albert On 02/08/2013 03:43 AM, Szilárd Páll wrote: Hi, If you have two GTX 590-s four devices should show up in nvidia-smi and mdrun should also show four devices detected. As nvidia-smi shows only tw

[gmx-users] npt equilbration + density

Dear gmx users My system is a single amino acid in water. I use two stage equilibration :  NVT (300 k) and NPT (300k , 1 barr) with position restrain. NPT simulation were done for 2.4 ns and 1.14 barr was obtained for pressure. but density is 974.031 . is this reasonable? should i change the

Re: [gmx-users] Reg:1 particles communicated to PME node 0 are more than 2/3 times the cut-off

On 2/8/13 9:12 AM, Shima Arasteh wrote: Doesn't that mean the npt should be done for a longer time? No. Look at the snippet of the .log file - the temperature at step zero is > 1800K! That indicates that the system is wildly unstable from the very start. Solutions to the problem are su

[gmx-users] Re: Adsorption layer of water molecules

The increase of the box volume occur in the beginning of the npt equilibration. The analysis of pressure was like that: Pressure nvt = fluctuates between 500 bar Pressure npt = fluctuates 1 bar Pressure in production stage = fluctuates 1 bar Actually, the problem is that water molecules go very f

Re: [gmx-users] npt equilbration + density

On 2/8/13 10:49 AM, Bahar Mehrpuyan wrote: Dear gmx users My system is a single amino acid in water. I use two stage equilibration : NVT (300 k) and NPT (300k , 1 barr) with position restrain. NPT simulation were done for 2.4 ns and 1.14 barr was obtained for pressure. but density is 974.

Re: [gmx-users] Re: Adsorption layer of water molecules

On 2/8/13 11:25 AM, ypca wrote: The increase of the box volume occur in the beginning of the npt equilibration. The analysis of pressure was like that: Pressure nvt = fluctuates between 500 bar Pressure npt = fluctuates 1 bar Pressure in production stage = fluctuates 1 bar Actually, the probl

Re: [gmx-users] Restarting simulation

On 2/8/13 12:31 AM, James Starlight wrote: Dear Gromacs Users! I try to restart canceled (by cnttl+z) simulation using cpt file mdrun -v -deffnm md_b2ar_APO -cpi md_b2ar_APO_prev after this I obtain error like Checksum wrong for 'md_b2ar_APO.log'. The file has been replaced or its conten

Re: [gmx-users] Re: Re: Error- Simulation box resizes during mdrun

On 2/8/13 2:51 AM, Bharath K. Srikanth wrote: Justin, You're right, the density of the box does increase during the simulation. How large is the increase in density? But I don't believe the water is particularly sparse, since I've never encountered this issue in previous simulations, when

Re: [gmx-users] MARTINI force-field in pulling simulations

Thanks Justin. The help has been much appreciated. Cheers, Davide On 7/02/13 8:46 PM, "Justin Lemkul" wrote: > > >On 2/7/13 2:29 PM, Davide Mercadante wrote: >> Thank you Justin, >> >> I guess this means that this kind of simulations is not possible >>without a >> modification of the forcefiel

Re: [gmx-users] npt equilbration + density

Thanks Justin for the reply.  i use SPC water model (12000 molecules). in literature there are different values for density which depend simulation time, number of water molecules , etc. (for example this paper : jcp.aip.org/resource/1/jcpsa6/v108/i24/p10220_s1) __

Re: [gmx-users] npt equilbration + density

On 2/8/13 11:54 AM, Bahar Mehrpuyan wrote: Thanks Justin for the reply. i use SPC water model (12000 molecules). in literature there are different values for density which depend simulation time, number of water molecules , etc. (for example this paper : jcp.aip.org/resource/1/jcpsa6/v108/i24

[gmx-users] Re: Adsorption layer of water molecules

Actually, I used trjconv (nojump) and these are the images of the run after the post-processing. I didn't understand very well what you mean with the box vectors of the starting and ending. When I used editconf, it has shown: box vectors : 7.205 10.465 11.742 (nm) new box vectors : 7.589 7.58

Re: [gmx-users] Re: Adsorption layer of water molecules

On 2/8/13 12:11 PM, ypca wrote: Actually, I used trjconv (nojump) and these are the images of the run after the post-processing. Then the output is exactly what you should be seeing. If you remove jumps, then molecules simply diffuse outward. There is nothing wrong at all with the traject

[gmx-users] Re: Adsorption layer of water molecules

Thank you very much! But when I use trjconv how you said, the water molecules are still in the cubic form, like in the beginning. Isn't there any problem? -- View this message in context: http://gromacs.5086.n6.nabble.com/Adsorption-layer-of-water-molecules-tp5005243p5005356.html Sent from the

Re: [gmx-users] Re: Adsorption layer of water molecules

On 2/8/13 12:49 PM, ypca wrote: Thank you very much! But when I use trjconv how you said, the water molecules are still in the cubic form, like in the beginning. Isn't there any problem? Why is that a problem? -Justin -- Justin A. Lemkul, Ph.D. R

[gmx-users] Re: Adsorption layer of water molecules

But are these modifies just a question about the visualization of the trajectory? Thank you very mych! -- View this message in context: http://gromacs.5086.n6.nabble.com/Adsorption-layer-of-water-molecules-tp5005243p5005358.html Sent from the GROMACS Users Forum mailing list archive at Nabble

Re: [gmx-users] Re: Adsorption layer of water molecules

On 2/8/13 1:10 PM, ypca wrote: But are these modifies just a question about the visualization of the trajectory? Yes. Please do some background reading on periodic boundary conditions if any of this is unfamiliar to you. -Justin -- Justin A. Lem

[gmx-users] genion error - No line with moleculetype 'SOL' found the [ molecules ] section of file ‘topol.top’

Dear All, I need to add 6 CL ions to make the system neutral but when I type the command line genion -s ions.tpr -o solv_ions.gro -p topol.top -pname NA -nname CL -nn 6 and choose group 15 (SOL), the error is Fatal error: No line with moleculetype 'SOL' found the [ molecules ] section of fi

Re: [gmx-users] GROMACS Error

Not sure - perhaps if you've edited this file by hand (or in an inappropriate editor) there's a tab-vs-space issue, or missing line ending on the final line. Mark On Fri, Feb 8, 2013 at 7:40 PM, Asma Mushtaq wrote: > Dear All, > > > > I need to add 6 CL ions to make the system neutral but when

Re: [gmx-users] Pulling and g_wham - Two analysis problems

On 2/8/13 6:00 AM, Steinbrecher, Thomas (IBG) wrote: Dear Gromacs users, I encountered two problems in using g_wham to calculate pmf curves from a pulling simulation. My system consists of a water molecule which is pulled through a bilayer (the reference group). I used gromacs 4.5.6 with the

[gmx-users] Diffusion beyond periodic boundary

Dear All I have performed MD run with periodic boundary condition, which system is consist of water and LJ particles. I would like to know the time dependence of the dislocated distance (diffusion) from the starting time (t=0). Firstly, I made pdb file of the trajectory, then calculated the dis

[gmx-users] genion error - No line with moleculetype 'SOL' found the [ molecules ] section of file ‘topol.top’ [only with PROTEIN-LIGAND complex]

Dear All, I need to add 6 CL ions to make the system neutral but when I type the command line genion -s ions.tpr -o solv_ions.gro -p topol.top -pname NA -nname CL -nn 6 I am able to add the ion easily to a protein or protein-peptide complex by using the above command line where I replace

[gmx-users] genion error { problem only with PROTEIN-LIGAND complex} - No line with moleculetype 'SOL' found the [ molecules ] section of file ‘topol.top’

Dear All, I need to add 6 CL ions to make the system neutral but when I type the command line genion -s ions.tpr -o solv_ions.gro -p topol.top -pname NA -nname CL -nn 6 I am able to add the ion easily to a protein or protein-peptide complex by using the above command line where I replace