Re: [gmx-users] lipid-SPC/SPCE interactions in lipid.itp (Tieleman website)

thanks Justin, best regards, 2013/3/5 Justin Lemkul > > > On 3/5/13 7:48 PM, fciocco wrote: > >> Hi, >> >> I have a quick question: >> >> the ;; lipid-SPC/SPCE interactions section : >> LOOW1 2.50200e-03 2.06700e-06 >>LOMOW1 2.50200e-03 2.06700e-06 >>LNLOW1

Re: [gmx-users] lipid-SPC/SPCE interactions in lipid.itp (Tieleman website)

On 3/5/13 7:48 PM, fciocco wrote: Hi, I have a quick question: the ;; lipid-SPC/SPCE interactions section : LOOW1 2.50200e-03 2.06700e-06 LOMOW1 2.50200e-03 2.06700e-06 LNLOW1 2.98000e-03 3.25900e-06 LCOW1 3.59800e-03 6.04400e-06 LH1OW

[gmx-users] lipid-SPC/SPCE interactions in lipid.itp (Tieleman website)

Hi, I have a quick question: the ;; lipid-SPC/SPCE interactions section : LOOW1 2.50200e-03 2.06700e-06 LOMOW1 2.50200e-03 2.06700e-06 LNLOW1 2.98000e-03 3.25900e-06 LCOW1 3.59800e-03 6.04400e-06 LH1OW1 3.26800e-03 5.71200e-06 LH2O

Re: [gmx-users] Re: BAR histogram results

On 3/5/13 10:56 AM, Sonia Aguilera wrote: Thank you Justin, I will add some lamda points between 0.1 to 0.5 and 0.5 to 0.9. I have a quick question related to recalculation. If I add, for example, a new lamda value of 0.3, I will set the following setting in the mdp file: init_lambda

[gmx-users] how to get pdb2gmx to use an arbitrarily located forcefield.ff directory?

Thank you, Francesco, for the assistance. However, I still can not get it to work (see below). Can you please specify exactly what you have done and perhaps show a listing of the directory structure? My command was: pdb2gmx -f protein.pdb -ff charmm36 I tried this in a number of ways, all event

Re: [gmx-users] how to get pdb2gmx to use an arbitrarily located forcefield.ff directory?

Hi Chris, I don't know if thngs changed in gromacs 4.6.x, but I succesfully did what you are triying to do setting the two variable GMXLIB and GMXDATA at the same time. Francesco 2013/3/5 Christopher Neale > Hello, > > I have downloaded the charmm36.ff directory and would like to use it with >

[gmx-users] only 4 zero eigvals for NMA

Dear, I am studying several protein fluctuation proteins using NMA (Normal Mode Analysis). In the mean time, I found out in many cases that NMA hessian matrix has about 3-4 zero eigenvalues even though having 6 zero eigenvalues are expected. I tried to reduce the tolerance level lesser than 10^-

[gmx-users] how to get pdb2gmx to use an arbitrarily located forcefield.ff directory?

Hello, I have downloaded the charmm36.ff directory and would like to use it with pdb2gmx. Everything works fine if I put it in the current directory or the share/gromacs/top directory of the binary that I am using. However, I'd like to be able to put the charmm36.ff directory in an arbitrary pl

Re: [gmx-users] GROMACS 4.6.1 released

On Tue, Mar 5, 2013 at 8:14 PM, Mark Abraham wrote: > *Hi GROMACS users, > > GROMACS 4.6.1 is officially released. It contains numerous bug fixes, some > simulation performance enhancements and some documentation updates. We > encourage all users to upgrade their installations from 4.6. > > You ca

[gmx-users] GROMACS 4.6.1 released

*Hi GROMACS users, GROMACS 4.6.1 is officially released. It contains numerous bug fixes, some simulation performance enhancements and some documentation updates. We encourage all users to upgrade their installations from 4.6. You can find the code, manual, release notes, installation instructions

[gmx-users] Re: BAR histogram results

Thank you Justin, I will add some lamda points between 0.1 to 0.5 and 0.5 to 0.9. I have a quick question related to recalculation. If I add, for example, a new lamda value of 0.3, I will set the following setting in the mdp file: init_lambda = 0.3 delta_lambda = 0 foreig

Re: [gmx-users] Error when extending simulation

On 03/05/2013 03:50 PM, Mark Abraham wrote: ... and your GROMACS version! 4.6 running on nodes with NVIDIA Keppler K10 and Intel E5 CPU Mark On Tue, Mar 5, 2013 at 3:11 PM, Justin Lemkul wrote: On 3/5/13 4:41 AM, sebastian wrote: On 03/04/2013 09:47 AM, sebastian wrote:

Re: [gmx-users] Error when extending simulation

... and your GROMACS version! Mark On Tue, Mar 5, 2013 at 3:11 PM, Justin Lemkul wrote: > > > On 3/5/13 4:41 AM, sebastian wrote: > >> On 03/04/2013 09:47 AM, sebastian wrote: >> >>> Hi Gromacs user, >>> >>> when I try to extend on of my simulations with >>> >>> mdrun -deffnm pdz_cis_NVT_disre_

Re: [gmx-users] Error when extending simulation

On 3/5/13 4:41 AM, sebastian wrote: On 03/04/2013 09:47 AM, sebastian wrote: Hi Gromacs user, when I try to extend on of my simulations with mdrun -deffnm pdz_cis_NVT_disre_equi_3 -cpi pdz_cis_NVT_disre_equi_3.cpt -append I get the following error Fatal error: Count mismatch for state e

Re: [gmx-users] Errors in compiling gromacs 4.5.6

See http://www.gromacs.org/Documentation/Installation_Instructions_4.5#Details_for_building_the_FFTW_prerequisite Mark On Tue, Mar 5, 2013 at 9:44 AM, Ekta Jain wrote: > Dear gmx Users, > I am very new to Linux and probably this is a very general thing i may be > seeking help for. > > I am faci

Re: [gmx-users] Re: gInstallation Problems with Gromacs4.6

On Tue, Mar 5, 2013 at 5:00 AM, Abhishek Acharya wrote: > Hello Mark > Sorry for the misunderstanding. Actually i did not provide any extra flags > to cmake. I generally edit the CMakeCache.txt file to provide the proper > paths. I somehow felt that was easier to do. I didn't think that could > le

Re: [gmx-users] g_hbond and contact

Thank you Sir. On Tue, Mar 5, 2013 at 4:33 PM, Erik Marklund wrote: > > On Mar 5, 2013, at 10:34 AM, Kavyashree M wrote: > > Sir, >> >> I used gromacs 4.6. I got the point - index file will tell how many >> contacts an >> atom has made during the trajectory. Whether it has made a contact with a

Re: [gmx-users] g_hbond and contact

On Mar 5, 2013, at 10:34 AM, Kavyashree M wrote: Sir, I used gromacs 4.6. I got the point - index file will tell how many contacts an atom has made during the trajectory. Whether it has made a contact with an atom only in once or all the time, in the whole trajectory, it will be mentioned.

[gmx-users] costu, fragment force field

I'm attempting to build a costume fragment library of beta amino acids with GAFF parametrization. I have converted the AMBER assigned parameters with acpype, built my .rtp .atp and .itp files. Everything works fine, until grompp, there i get a lot of "No default Ryckaert-Bell. types" errors. The pr

Re: [gmx-users] Error when extending simulation

On 03/04/2013 09:47 AM, sebastian wrote: Hi Gromacs user, when I try to extend on of my simulations with mdrun -deffnm pdz_cis_NVT_disre_equi_3 -cpi pdz_cis_NVT_disre_equi_3.cpt -append I get the following error Fatal error: Count mismatch for state entry disre_rm3tav, code count is 0, fi

Re: [gmx-users] g_hbond and contact

Sir, I used gromacs 4.6. I got the point - index file will tell how many contacts an atom has made during the trajectory. Whether it has made a contact with an atom only in once or all the time, in the whole trajectory, it will be mentioned. Am I right? So from the problem I had, can I say that n

[gmx-users] Errors in compiling gromacs 4.5.6

Dear gmx Users,I am very new to Linux and probably this is a very general thing i may be seeking help for. I am facing problems in compiling GROMACS after installing the prerequisites (fftw-3.3.3)I get the following error towards the end of "make"# makerecompile with -fPIC/usr/local/lib/libfftw3f.

Re: [gmx-users] g_hbond and contact

To clarify: the -hbn output is not very indicative of how many contacts there were since some of them could be present in one frame but absent in 99. The -num option, however, provides the number of contacts over time, and its time average probably tells you much more in this case. Wh

Re: [gmx-users] Time-Dependent Electric Field

From the manual it seems that oscillating electric fields are not yet implemented, which surprised me. I've seen colleagues use such in gromacs, but that may have been in-house modifications. Should be fairly simple to implement though. Erik On Mar 4, 2013, at 11:30 PM, raquick wrote: Gr