[gmx-users] Implementing GoIP parameters in OPLSAA

2016-04-05 Thread ingram
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

Re: [gmx-users] WARNING: Incomplete frame

2016-04-05 Thread Brett
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.

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

2016-04-05 Thread Michał Kadlof
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] WARNING: Incomplete frame

2016-04-05 Thread Brett
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

2016-04-05 Thread Justin Lemkul
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] Implementing GoIP parameters in OPLSAA

2016-04-05 Thread Justin Lemkul
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

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

2016-04-05 Thread Justin Lemkul
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

[gmx-users] several basic questions on GROMACS

2016-04-05 Thread Brett
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] Simulations enclosed in sphere and arbitrary defined non standard interactions

2016-04-05 Thread Justin Lemkul
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

Re: [gmx-users] WARNING: Incomplete frame

2016-04-05 Thread Justin Lemkul
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] xpmtps gives empy eps file

2016-04-05 Thread Justin Lemkul
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:

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

2016-04-05 Thread Justin Lemkul
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

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

2016-04-05 Thread ABEL Stephane 175950
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

2016-04-05 Thread Justin Lemkul
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] xpmtps gives empy eps file

2016-04-05 Thread Nikhil Maroli
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] several basic questions on GROMACS

2016-04-05 Thread Brett
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] several basic questions on GROMACS

2016-04-05 Thread Justin Lemkul
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

Re: [gmx-users] pdb2gmx error

2016-04-05 Thread ABEL Stephane 175950
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] maxh mdrun option does not work with REMD simulation

2016-04-05 Thread Maud Jusot
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] empty aminoacids.n.tdb and aminoacids.c.tdb files for Amber99*

2016-04-05 Thread Mark Abraham
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] gromacs.org_gmx-users Digest, Vol 144, Issue 18

2016-04-05 Thread Mijiddorj Batsaikhan
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 >

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

2016-04-05 Thread Mijiddorj Batsaikhan
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] maxh mdrun option does not work with REMD simulation

2016-04-05 Thread Mark Abraham
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] appropriate position restraint for stability of alpha helix

2016-04-05 Thread Tsjerk Wassenaar
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] npt equilibration nanotubes

2016-04-05 Thread ANAND AMITKUMAR DHARIA
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 5.1.2 installation problem

2016-04-05 Thread Husen R
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] mdrun -rerun to obtain the non-bond interaction energy among energy groups

2016-04-05 Thread Dai Ling (IHPC)
Dear gmx-user: I want to plot the non-bond interaction energy between energy-groups. With reading from the history of this mailing-list, I need to use "rerun" to obtain these values. Since I have set all the energy groups in .mdp file initially. So that, after the first mdrun, I just use the

[gmx-users] Gromacs 5.1.2 installation problem

2016-04-05 Thread Husen R
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

Re: [gmx-users] Gromacs 5.1.2 installation problem

2016-04-05 Thread James Graham
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] pdb2gmx error

2016-04-05 Thread ABEL Stephane 175950
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

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

2016-04-05 Thread David Newman
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] xpmtps gives empy eps file

2016-04-05 Thread Nikhil Maroli
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