Re: [gmx-users] Is charmm GUI ideal for membrane building

Hi Amit, What membrane and what time scale are you talking about? Complex membranes may take microseconds to equilibrate. Cheers, Tsjerk On Jun 13, 2016 06:13, wrote: > Hello everyone, > I built a lipid membrane in Charmm-GUI and tried to equilibrate it in >

[gmx-users] Is charmm GUI ideal for membrane building

Hello everyone, I built a lipid membrane in Charmm-GUI and tried to equilibrate it in GROMACS 5.1.2. But the total energy goes on decreasing. Is it normal or should I try building the membrane by other methods. Thanks in advance, Amit Behera -- This message has been scanned for viruses and

Re: [gmx-users] Extending the REMD

Dear Mark, Sorry to disturb you again. What you mean is that the option “reseed -1” is used only once at the first start of REMD and I do not need to use it again for the forthcoming extended REMD simulation ? I wonder why? > 在 2016年6月12日，下午10:53，Mark Abraham

Re: [gmx-users] problem about distance restraint in REMD simulation

Dear Mark, Thank you for your replay. It is very usefull for me. Juan > -原始邮件- > 发件人: "Mark Abraham" > 发送时间: 2016-06-12 22:51:52 (星期日) > 收件人: gmx-us...@gromacs.org > 抄送: > 主题: Re: [gmx-users] problem about distance restraint in REMD simulation > > Hi, > >

[gmx-users] Decreased Area Per Lipid for Lipid Bilayer obtained from CHARMM-GUI

Hello GROMACS Users, I have modelled a mixed bilayer system consisting of 35 DPPC lipids and one POPA lipid (in each monolayers) using CHARMM-GUI. NPT ensemble was chosen while creating the model. TIP3 water model was used for modeling. I did not use surface tension for the membrane. I have

Re: [gmx-users] problem compiling template

Use -dfftw_library=/path/to/libfftw3.so -dfftw_include_dir=path/to/includedirectory Pada tanggal 12 Jun 2016 21.55, "Teemu Murtola" menulis: > Hi, > > On Fri, Jun 10, 2016 at 8:51 PM Michael Brunsteiner < > michael.brunstei...@tugraz.at> wrote: > > > I just installed a

Re: [gmx-users] mdrun error

Hi, Is your box changing shape? You've switched from isotropic to anisotropic, and to a thermostat that is not tolerant of changes to the size/shape of the box. Change one thing at a time. Mark On Sun, Jun 12, 2016 at 8:09 PM mahdiyeh poorsargol < poorsargol@gmail.com> wrote: > Dear gmx

[gmx-users] mdrun error

Dear gmx users, I am using gromacs 4.6.5 to simulate a system including: graphene + water + surfactant. I used the box with size 7.4,7.4,9.4 (nm3) and a cutoff distance of 1.2 nm. I have done nvt with Berendsen thermostat for 1 ns , npt with Berendsen thermostat and Berendsen barostat for 2 ns

Re: [gmx-users] frame with lowest energy

Hello there, Concerning to the issue raised by Sana and "gmx cluster", what would be the potential known useful geometric criterion of amino acids in each of below systems: 1) A single amino acid in aqueous solution? 2) A single amino acid adsorbed on a solid surface in aqueous solution?

Re: [gmx-users] problem compiling template

Hi, On Fri, Jun 10, 2016 at 8:51 PM Michael Brunsteiner < michael.brunstei...@tugraz.at> wrote: > I just installed a pristine gromacs 5.1.2, on my lubuntu 64bit vanilla > desktop, as in: > > prompt> cmake .. -DGMX_GPU=ON > -DCMAKE_INSTALL_PREFIX=/usr/local/gromacs-5.1.2-bin

Re: [gmx-users] an error for mdrun

Hi, Why should it be stable? Mark On Sun, Jun 12, 2016 at 4:01 PM <15110700...@fudan.edu.cn> wrote: > > > Hello, > everyone. > I recently created a system for PDE2 , a protein containing two ions > (Zn and Mg) in its pocket. The distance between the two ions is about 3.9 > Å. Thus

Re: [gmx-users] Extending the REMD

Hi, On Sun, Jun 12, 2016 at 3:22 PM YanhuaOuyang <15901283...@163.com> wrote: > Dear Gromacs users, > > I want to extend my REMD simulation to another 2 ns after a short REMD is > completed with Gromacs 5.0.2 > > my commands: > gmx convert-tpr -s previous.tpr -extend 2000 -o next.tpr > gmx mdrun

Re: [gmx-users] problem about distance restraint in REMD simulation

Hi, That check is unfortunately a little bit overzealous. I have proposed a fix for the upcoming 5.1.3 release. If you want to fix your 4.6 version (but you should anyway not start new work on such old versions of GROMACS) then you can go to src/gmxlib/disre.c and change if (dd->dr_tau

[gmx-users] an error for mdrun

Hello, everyone. I recently created a system for PDE2 , a protein containing two ions (Zn and Mg) in its pocket. The distance between the two ions is about 3.9 Å. Thus the strong electrostatic force between them made the system blow up. One part of my .mdp parameters are here:

[gmx-users] Extending the REMD

Dear Gromacs users, I want to extend my REMD simulation to another 2 ns after a short REMD is completed with Gromacs 5.0.2 my commands: gmx convert-tpr -s previous.tpr -extend 2000 -o next.tpr gmx mdrun -s next.tpr -cpi state.cpt -multi 30 -replex 1000 -reseed -1 I wonder if the option

Re: [gmx-users] [gmx-developers] GTX 680 non detected on OS X

Hi Szilárd, thanks for the shell trick (it worked smoothly). I’m happy to report I tamed it (partly, this is an "ad hoc” fix needs to have /usr/local/cuda symlink to the actual installation) with this patch (applied on release-2016 branch): uliano@MacPro:~/local/src/gromacs$ git log -p -1

[gmx-users] problem about distance restraint in REMD simulation

Dear Users: I have a system with four distance restraints to maintain a hydrogen-bonding network in REMD simulation. While when I applied the distance restraint, the REMD simulation is only ok when applied single CPU for each replica. When I applied more than one CPU for each replica, there

[gmx-users] adding extra ions to charmm gui output

Dear all , For studying transport properties of the peptide tube have made system using charmm-gui.later i added three pottasium ion inside the channel using YASARA software and added sufficent neautral charges.neccessary entries are made in topology and atp,itp (ff is charmm 36). when i execute