[gmx-users] adding hydrogen atoms into a POPC membrane

Dear gromacs users, I just ran a CG simulation of a system consisting in a protein embedded in a POPC membrane solvated in water. After that i ran the script .initram to obtain an AA representation of my system (gromos54a7), but sadly i couldn’t find a *.itp with the description of the hydro

Re: [gmx-users] output dispersion correction and coul. recip. for energy groups

Yes, but before you can compute a quantity you need to define an expression for it... For example, the derivation of the dispersion correction (see manual) starts with "assuming a homogeneous distribution of particles." You can maybe come up with some multiple-rerun zeroing-parameters additive sche

Re: [gmx-users] output dispersion correction and coul. recip. for energy groups

Hi On Fri, Dec 12, 2014 at 4:17 PM, Mark Abraham wrote: > > On Fri, Dec 12, 2014 at 10:42 PM, Yongchul Chung > wrote: > > > > Hi gmx-users, > > > > I am using grommacs-5.0.2 with gpu acceleration. I am simulating two > energy > > groups. > > > > Is there a way to output reciprocal coulomb and di

Re: [gmx-users] output dispersion correction and coul. recip. for energy groups

On Fri, Dec 12, 2014 at 10:42 PM, Yongchul Chung wrote: > > Hi gmx-users, > > I am using grommacs-5.0.2 with gpu acceleration. I am simulating two energy > groups. > > Is there a way to output reciprocal coulomb and dispersion correction > between each energy groups? It is odd to see GROMACS repor

[gmx-users] output dispersion correction and coul. recip. for energy groups

Hi gmx-users, I am using grommacs-5.0.2 with gpu acceleration. I am simulating two energy groups. Is there a way to output reciprocal coulomb and dispersion correction between each energy groups? It is odd to see GROMACS reports LJ and Coulombic interaction energies between two groups without dis

Re: [gmx-users] with 5.0: file INSTALL cannot find gmx

Am 12/12/14 19:40, schrieb Johnny Lu: > Oh, and what version of cmake are you using? > > If that is too old, you can compile a newer version of cmake and then use > that. Hey, that was a good hint!! I used 2.8.12.2 before. I just gave it a try with the latest 3.02 - and it worked! So many thank

Re: [gmx-users] Segfault on energy minimization

I caught the problem, i had my silver atoms too tight inside the box causing them to collide in the boundaries. Many thanks Sr. Abraham. On Friday 12 December 2014 20:30:29 Mark Abraham wrote: > Hi, > > The "Fmax= 2.35818e+10, atom= 214" in the output says you are > http://www.gromacs.org/Docume

Re: [gmx-users] pdb2gmx atom not found

On 12/12/14 12:52 PM, xy21hb wrote: Dear all, I am introducing a residue named ABC into AMBER03 force field. I built up the aminoacids.rtp and aminoacids.hdb file, but when I pdb2gmx, it gives, " Atom HB1 not found in rtp database in residue ABC, it looks a bit like HB " I am pretty sure I u

Re: [gmx-users] protein-ligand complex fatal error

On 12/12/14 9:19 AM, Yaser Hosseini wrote: hi i just want to run mdrun -v deffnm nvt i run every command in this tutorials http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex_old/index.html but at the end i got two errors : There are: 247500 Atoms Charge group

[gmx-users] Fw: pdb2gmx atom not found

Forwarding messages From: "xy21hb" Date: 2014-12-13 01:52:03 To: "gmx-us...@gromacs.org" Subject: [gmx-users] pdb2gmx atom not found Dear all, I am introducing a residue named ABC into AMBER03 force field. I built up the aminoacids.rtp and aminoacids.hdb file, but

Re: [gmx-users] Segfault on energy minimization

Hi, The "Fmax= 2.35818e+10, atom= 214" in the output says you are http://www.gromacs.org/Documentation/Terminology/Blowing_Up, likely because you've constructed initial conditions that don't make sense, leading to forces many orders of magnitude higher than you probably intend. Start with the simp

[gmx-users] Segfault on energy minimization

Dear Gromacs users, I'm trying to launch a MD calculation involving silver atoms, but when I run the energy minimization gromacs crashes into a Segmentation Fault. This is: when I type: mpirun -H nodo1 -np 8 gmx_mpi mdrun -deffnm solvent_test y get this output: http://pastebin.com/JeNqVFgc[1]

Re: [gmx-users] with 5.0: file INSTALL cannot find gmx

Oh, and what version of cmake are you using? If that is too old, you can compile a newer version of cmake and then use that. On Fri, Dec 12, 2014 at 1:35 PM, Johnny Lu wrote: > > maybe ... compile it on the head node of the cluster, and hope it has a > local storage? > > fftpack is slow, and let

Re: [gmx-users] with 5.0: file INSTALL cannot find gmx

maybe ... compile it on the head node of the cluster, and hope it has a local storage? fftpack is slow, and let gromacs build its own fftw3 library is better. I don't know if the fftpack code of gromacs is old. May be Location of where you run cmake/CMakeFiles/CMakeError.log will tell a bit mor

Re: [gmx-users] with 5.0: file INSTALL cannot find gmx

Am 12/12/14 19:07, schrieb Mark Abraham: > Hi, > > I have seen similar behaviour on "interesting" setups, e.g. where the same > physical file system has different logical locations, but I don't know > where the issue is. $(pwd) should be expanded by the shell before cmake > sees it, so how a wro

Re: [gmx-users] with 5.0: file INSTALL cannot find gmx

Am 12/12/14 19:07, schrieb Mark Abraham: > Hi, > > I have seen similar behaviour on "interesting" setups, e.g. where the same > physical file system has different logical locations, but I don't know > where the issue is. $(pwd) should be expanded by the shell before cmake > sees it, so how a wro

Re: [gmx-users] with 5.0: file INSTALL cannot find gmx

Hi, I have seen similar behaviour on "interesting" setups, e.g. where the same physical file system has different logical locations, but I don't know where the issue is. $(pwd) should be expanded by the shell before cmake sees it, so how a wrong path could get into cmake_install.cmake is a mystery

[gmx-users] pdb2gmx atom not found

Dear all, I am introducing a residue named ABC into AMBER03 force field. I built up the aminoacids.rtp and aminoacids.hdb file, but when I pdb2gmx, it gives, " Atom HB1 not found in rtp database in residue ABC, it looks a bit like HB " I am pretty sure I use HB instead of HB1, and there is no at

Re: [gmx-users] with 5.0: file INSTALL cannot find gmx

I'm not sure what happened, but so far when i install, i use full path instead of $(pwd) and it was fine for gromacs 4.6 and 5.0, 5.0.2. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read ht

[gmx-users] with 5.0: file INSTALL cannot find gmx

Hi all, I am having trouble to make install Gromacs 5.0x under Linux. make install fails with: CMake Error at src/programs/cmake_install.cmake:42 (FILE): file INSTALL cannot find "/home/waxs/opt/gmx/5.03-rotmax/bin/gmx". Call Stack (most recent call first): src/cmake_install.cmake:40 (INCLUDE

Re: [gmx-users] pmetune and restarting

On Fri, Dec 12, 2014 at 5:23 PM, Johnny Lu wrote: > > Hi. > > I notice that after I stop a simulation by specifying the number of hours > that it runs with -maxh, > and then restarting the simulation, at the beginning of each restart, the > pme is tuned again. > > Will that cause any error if I pe

[gmx-users] pmetune and restarting

Hi. I notice that after I stop a simulation by specifying the number of hours that it runs with -maxh, and then restarting the simulation, at the beginning of each restart, the pme is tuned again. Will that cause any error if I periodically restart the simulation? How big is the error? Is it pos

Re: [gmx-users] Question about GPU acceleration in GROMACS 5

On Fri, Dec 12, 2014 at 3:47 PM, Tomy van Batis wrote: > > Hi Mark > > Thanks for your detailed reposponce. > > I still don't see the reason for the GPU loading to be only around 50%, but > also why does this number increases with increasing CPU cores. > > For example, when using 1 CPU (-ntomp 1 i

Re: [gmx-users] trjconv precision lost from double to single conversion

On Fri, Dec 12, 2014 at 4:31 PM, Johnny Lu wrote: > > Hi. I'm using gromacs 4.6.7 > > If the trr trajectory file is from double precision calculation, and I use > single precision trjconv to make a single precision trr trajectory, how > much precision will I lose in position and in force? > You'l

Re: [gmx-users] gromacs on GPU

Hi, Szilárd, Thank you for your reply. I tried solution i) and still got the same errors. I will try to do solution ii) Where can I get sample input files that result in obtain better performance on GPU than on CPU? Best, Shaohao On 12/09/2014 03:05 PM, Szilárd Páll wrote: Hi Shaohao,

Re: [gmx-users] trjconv precision lost from double to single conversion

nevermind the 2nd question. it does reduce to about 1/10 size. On Fri, Dec 12, 2014 at 10:41 AM, Johnny Lu wrote: > > When I test the disk space that I would save by getting rid the water in > the trajectory, I found that only make the trajectory 1/4 as large as the > original. > The trajectory h

Re: [gmx-users] trjconv precision lost from double to single conversion

When I test the disk space that I would save by getting rid the water in the trajectory, I found that only make the trajectory 1/4 as large as the original. The trajectory has both position and force. Yet, the proteins only have about 1/10 the number of atoms of the whole system. Group 0 (

[gmx-users] trjconv precision lost from double to single conversion

Hi. I'm using gromacs 4.6.7 If the trr trajectory file is from double precision calculation, and I use single precision trjconv to make a single precision trr trajectory, how much precision will I lose in position and in force? 1, 0.1, 0.01, or 0.001 angstrom and Newton? Is the lost of precision

Re: [gmx-users] Question about GPU acceleration in GROMACS 5

Hi, On 12 Dec 2014, at 15:47, Tomy van Batis wrote: > Hi Mark > > Thanks for your detailed reposponce. > > I still don't see the reason for the GPU loading to be only around 50%, but > also why does this number increases with increasing CPU cores. > > For example, when using 1 CPU (-ntomp 1 i

Re: [gmx-users] Question about GPU acceleration in GROMACS 5

Hi Mark Thanks for your detailed reposponce. I still don't see the reason for the GPU loading to be only around 50%, but also why does this number increases with increasing CPU cores. For example, when using 1 CPU (-ntomp 1 i nthe mdrun) , the GPU loading is only about 25-30%, although with 4 CP

[gmx-users] protein-ligand complex fatal error

hi i just want to run mdrun -v deffnm nvt i run every command in this tutorials http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex_old/index.html but at the end i got two errors : There are: 247500 Atoms Charge group distribution at step 0: 20986 20508 20732 20838

Re: [gmx-users] Fwd: Question about GPU acceleration in GROMACS 5

Hi, Only the short-ranged non-bonded work is offloaded to the GPU, but that's almost all the force-based work you are doing. So it is entirely unsurprising that the work done on the GPU takes a lot longer than it does on the CPU. That warning is aimed at the more typical PME-based simulation where

[gmx-users] Fwd: Question about GPU acceleration in GROMACS 5

Dear all I am working with a system of about 200.000 particles. All the non-bonded interactions on the system are Lennard-Jones type (no Coulomb). I constrain the bond-length with Lincs. No torsion or bending interactions are taken into account. I am running the simulations on a 4-core Xeon® E5-

[gmx-users] How to define the covalent bonds between ligand and protein

​Dear All, I am trying to perform protein-ligand MD where the ligand is covalently bonded to the receptor. I have seen few earlier post from other users who are trying to solve such complexes. Few days ago few gromacs users suggested to define a new residue to the force fields. However, it is ve

Re: [gmx-users] Segmentation fault error

Yes, seems like blowing up, but I would run it on another machine to be sure. Mark On Fri, Dec 12, 2014 at 9:03 AM, Seyed Mojtaba Rezaei Sani < s.m.rezaeis...@gmail.com> wrote: > > Hi Mark, > > Thanks for your response. I use a rather old version of GROMACS, 4.5.4. > Please find the md.log file i

[gmx-users] Using g_densmap

Dear all, I am studying the effect of different ion binding to the sites of a double stranded DNA . I am using GROMACS 4.5.6 and CHARMM force field for my MD simulations. I have three different simulation results with sodium, TMA and Choline ions. what I want to do is to make number de

Re: [gmx-users] Segmentation fault error

Hi Mark, Thanks for your response. I use a rather old version of GROMACS, 4.5.4. Please find the md.log file in the following link: https://www.dropbox.com/s/bbmqln6oqjyus0b/md.log?dl=0 I also have to mention that due to reaching the machine precision I could not minimized the energy of the system