Re: [gmx-users] Gromacs 5.1.2 installation problem

Hello James, Thank you for your reply and valuable information. I tried running "gmx [command]" and it works. Sorry for this fundamental question. Regards, Husen On Tue, Apr 5, 2016 at 4:11 PM, James Graham wrote: > Hi Husen, > > In GROMACS version 5.1 the default

[gmx-users] npt equilibration nanotubes

Hello, For those who have simulated with nanotubes, how have you performed an nPT equilibration of your systems. I have used a freeze group on my nanotube, however, I know this is incompatible for pressure coupling. Thanks, Anand -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 144, Issue 18

I think that Husen, you shoud add your gromacs installed director /usr/local/gromacs/bin: to $PATH in /etc/bashrc. On Apr 5, 2016 6:00 PM, wrote: > Send gromacs.org_gmx-users mailing list submissions to >

Re: [gmx-users] appropriate position restraint for stability of alpha helix

Hi Mijiddorj, For a biologically stable alpha-helix, you should not use any restraints. If you want to stabilize a helix that is known to fold/unfold, then try something not too stiff. Usually like 100 kJ/mol/nm^2 should already do. But again, don't try to 'fix' a force field in this way.

[gmx-users] appropriate position restraint for stability of alpha helix

Dear users, Hello. I would like to simulate different length of alpha helices. I would like to find position restrain and other important parameters for stability of helix. What value of restrain appropriate for stable helix? Mijiddorj -- Gromacs Users mailing list * Please search the archive

Re: [gmx-users] empty aminoacids.n.tdb and aminoacids.c.tdb files for Amber99*

Hi, Building whole capping groups has never been in scope for pdb2gmx, and particularly not for the AMBER force fields, which use specially parameterised charged amino acid termini (for example). IIRC there are also some neutral capping groups in .rtp files that are usable as residues, but

Re: [gmx-users] maxh mdrun option does not work with REMD simulation

Hi, It should work, but apparently doesn't. Please open an issue at redmine.gromacs.org and include a tarball of your tpr files so we can see the problem happen and fix it. Meanwhile, I suggest the approach of using gmx grompp to construct a run that will complete in the maximum time you can

Re: [gmx-users] maxh mdrun option does not work with REMD simulation

Hello again I still don’t manage to restart correctly REMD simulation (see my previous message) but I can add some details. When it restarts, gromacs doesn’t create new checkpoint files (no matter –cpt option is), and doesn’t stop at maxh time. I tried with 3 different versions of gromacs

Re: [gmx-users] WARNING: Incomplete frame

Dear Justin, Will you please write out the restart command for me? I am afraid without your written command I cannot do it. Brett At 2016-04-05 22:06:57, "Justin Lemkul" wrote: > > >On 4/5/16 10:04 AM, Brett wrote: >> Dear Justin, >> >> WIll you please give a reply

Re: [gmx-users] WARNING: Incomplete frame

On 4/5/16 10:19 AM, Brett wrote: Dear Justin, Will you please write out the restart command for me? I am afraid without your written command I cannot do it. Have you searched the archive? Have you read any recent posts to this list? I actually responded to someone else with the exact

Re: [gmx-users] WARNING: Incomplete frame

Dear Justin, WIll you please give a reply for the following question? Most probably I need to restart my MD from the beginning? Brett At 2016-04-05 17:18:31, "Brett" wrote: Dear All, After energy minimization and equilibration, I started a 10 ns production MD.

Re: [gmx-users] WARNING: Incomplete frame

On 4/5/16 10:04 AM, Brett wrote: Dear Justin, WIll you please give a reply for the following question? Most probably I need to restart my MD from the beginning? Restart from the last checkpoint and use -cpi -append. mdrun will overwrite the broken frames. No need for trjcat, trjconv,

Re: [gmx-users] several basic questions on GROMACS

On 4/5/16 9:34 AM, Brett wrote: Dear Justin, Suppose at the end of NVT equilibation and before the start of the following NPT equilibation, I intentionally (or by accident) delete the nvt_prev.cpt file from the directory, does it affect the run of the NPT equilibation step? No. Once an

Re: [gmx-users] several basic questions on GROMACS

Dear Justin, Suppose at the end of NVT equilibation and before the start of the following NPT equilibation, I intentionally (or by accident) delete the nvt_prev.cpt file from the directory, does it affect the run of the NPT equilibation step? Brett At 2016-04-05 21:27:41, "Justin

Re: [gmx-users] xpmtps gives empy eps file

Thanks, it is worked in another system but eps file was very poor quality ,i will check about .m2p -- 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

Re: [gmx-users] pdb2gmx error

Indeed Justin I have tried to add the entries for the capped groups in the Amber99SB-ILDN force field (like in the charmm*.ff) since they are not present in aminoacids.n.tdb and aminoacids.c.tdb, so I think I have broken something Stéphane On 4/5/16 6:47 AM, ABEL Stephane 175950

Re: [gmx-users] Simulations enclosed in sphere and arbitrary defined non standard interactions

On 4/5/16 9:29 AM, Michał Kadlof wrote: Hello, I would like to run my simulations inside closed sphere. It may be something like soft-walls potential (0 inside a sphere, and proportional to r^2 outside sphere with force directed to the center of sphere) or something similar. Is it possible

[gmx-users] Simulations enclosed in sphere and arbitrary defined non standard interactions

Hello, I would like to run my simulations inside closed sphere. It may be something like soft-walls potential (0 inside a sphere, and proportional to r^2 outside sphere with force directed to the center of sphere) or something similar. Is it possible with Gromacs? I'm not afraid to mess up

Re: [gmx-users] several basic questions on GROMACS

On 4/5/16 9:24 AM, Brett wrote: Dear All, Based on the on-line Lysozyme tutorial, I started a MD from energy minimization to NVT equlibation to NPT equlibration, and I am now in the production MD step. When I checked my Directory containing all the MD files for the whole MD process, I find

[gmx-users] empty aminoacids.n.tdb and aminoacids.c.tdb files for Amber99*

Hello again I have noticed that in case of the amber* forcefields (in gromacs v504) the aminoacids.n.tdb and aminoacids.c.tdb files are empty* so it is not possible to construct easily a capped AA with the pdb2gmx -ter command without using a rtp file (and it is very painful). So does anyone

Re: [gmx-users] pdb2gmx error

On 4/5/16 6:47 AM, ABEL Stephane 175950 wrote: Hello, When i use pdb2gmx (v.504) and 12 AA long peptide with the Amber99SB-ILDN force field, I have the error : Fatal error: tpA = 53191, i= 0 in print_atoms I have no idea what does this message mean. Could you help me? This shouldn't

Re: [gmx-users] extending npt step/generating output from crashed/fatal error-based quit session.

On 4/5/16 8:29 AM, David Newman wrote: While running the npt step gromacs encountered the following error about 4-6ps before the end of the mdrun: File input/output error: npt_step46830.cpt I tried the commands for extending the simulation but these seem setup for the production runs as

Re: [gmx-users] xpmtps gives empy eps file

On 4/5/16 8:43 AM, Nikhil Maroli wrote: Dear all, while analyzing secondary structure i have invoked the command gmx xpm2ps -f dssp.xpm -o dssnew.eps There is 1 matrix in dssp.xpm Matrix 0 is 1001 x 449 Auto tick spacing for X-axis: major 2, minor 5000 Auto tick spacing for Y-axis:

[gmx-users] several basic questions on GROMACS

Dear All, Based on the on-line Lysozyme tutorial, I started a MD from energy minimization to NVT equlibation to NPT equlibration, and I am now in the production MD step. When I checked my Directory containing all the MD files for the whole MD process, I find there is a "mdout.mdp". Is my

Re: [gmx-users] Implementing GoIP parameters in OPLSAA

On 4/5/16 9:14 AM, ingram wrote: Dear GROMACS gremlins, I am trying in vain to implement the GoIP parameters for a gold-peptide interface in the OPLSAA ff. To begin with I am just trying to get the paramteres working for only a 3x3 Au slab. My .pdb file looks like this: OMPNDNew structure

[gmx-users] Implementing GoIP parameters in OPLSAA

Dear GROMACS gremlins, I am trying in vain to implement the GoIP parameters for a gold-peptide interface in the OPLSAA ff. To begin with I am just trying to get the paramteres working for only a 3x3 Au slab. My .pdb file looks like this: OMPNDNew structure COMPND 1Created by VESTA

[gmx-users] xpmtps gives empy eps file

Dear all, while analyzing secondary structure i have invoked the command gmx xpm2ps -f dssp.xpm -o dssnew.eps There is 1 matrix in dssp.xpm Matrix 0 is 1001 x 449 Auto tick spacing for X-axis: major 2, minor 5000 Auto tick spacing for Y-axis: major 50, minor 10 Set the x-size of the box

[gmx-users] extending npt step/generating output from crashed/fatal error-based quit session.

While running the npt step gromacs encountered the following error about 4-6ps before the end of the mdrun: File input/output error: npt_step46830.cpt I tried the commands for extending the simulation but these seem setup for the production runs as it quite complaining about the lack of

[gmx-users] pdb2gmx error

Hello, When i use pdb2gmx (v.504) and 12 AA long peptide with the Amber99SB-ILDN force field, I have the error : Fatal error: tpA = 53191, i= 0 in print_atoms I have no idea what does this message mean. Could you help me? Thanks -- Gromacs Users mailing list * Please search the archive

Re: [gmx-users] Gromacs 5.1.2 installation problem

Hi Husen, In GROMACS version 5.1 the default program naming scheme was changed so that everything is now part of the executable 'gmx'. Because of this you need to use 'gmx pdb2gmx' (and e.g. 'gmx grompp', 'gmx mdrun') instead. The change was actually made in version 5.0, but they left an

[gmx-users] Gromacs 5.1.2 installation problem

Dear all, I already installed gromacs-5.1.2 succesfully with the following instruction : tar xfz gromacs-5.1.2.tar.gz cd gromacs-5.1.2 mkdir build cd build cmake .. -DGMX_BUILD_OWN_FFTW=ON -DGMX_MPI=ON make make check sudo make install source /usr/local/gromacs/bin/GMXRC However, after