[gmx-users] invalid angle type 0

Dear all, I 've prepared POPC and protein with ffG53a6 forcefield. I've also built the ligand in the protein with ffG53a6, but it is not working. Many atom types in the ligand which i work on is not found in ffG53a6*.itp but if i change the forcefield to ffgmx, it work fine. I have tried to add-i

Re: [gmx-users] invalid angle type 0

Bing Bing wrote: Dear all, I 've prepared POPC and protein with ffG53a6 forcefield. I've also built the ligand in the protein with ffG53a6, but it is not working. Many atom types in the ligand which i work on is not found in ffG53a6*.itp but if i change the forcefield to ffgmx, it work fine. I

RE: [gmx-users] invalid angle type 0

Bing Bing, There is a topology available for POPC with ffG53a6 in the user contribution section. Published in: Kukol, A., 2009. Lipid models for united-atom molecular dynamics simulations of proteins. J. Chem. Theor. Comput.,5(3), 615-626. However, it currently doesn't work with Gromacs 4, but

Re: [gmx-users] Periodic Boundary Condition Issues

Try combining indices with that, use "make_ndx -h". --Omer. Koby Levy research group, Weizmann Institute of Science. FAX: 972-77-444-7905 http://www.weizmann.ac.il/sb/faculty_pages/Levy/ On Wed, Jul 22, 2009 at 18:27, Justin A. Lemkul wrote: > The trjconv -pbc options were designed to fix this

[gmx-users] Re: Some questions on Tabulated Dihedral Potential

Hi Ran, are you sure the derivative is calculated as: der = (y[N+1] - y[N-1]) * 0.5 * deltaX and not as: der = (y[N+1] - y[N-1]) * 0.5 / deltaX ? The last calculation makes a little more sense to me... -Johannes Ran Friedman wrote: Hi, The numerical deri

Re: [gmx-users] Re: Some questions on Tabulated Dihedral Potential

Hi Johannes, Thanks for the correction - you're right of course (when deltaX = 1 it's the same). To be closer to the gromacs code it's der = (y[N+1] - y[N-1]) * 0.5 * tabscale where tabscale = number of points per nm (or degree for angles/dihedrals). Ran. Johannes Kamp wrote: > Hi Ran, > > are

Re: [gmx-users] pull.ppa doesn't work

accomp lin wrote: hi everyone, I;m using umbrella sampling to calculate PMF My system is DPPC + water + protein In pull.ppa, I set runtype = umbrella ，reftype = com_t0， K1 = 5000 ，Pos1 = 0.0 0.0 6.0 However this came out when I finally type mdrun :

[gmx-users] using two different combination rules for the LJ potentia

Thank you so much for the kind reply. I made a mistake in my previous posting - I am dealing with combination rule 1 and the combination rule 2. Initially I converted the parameters according to section 5.3.3 of the manual and when I did some tests to verify my force-field, the minimum of t

Re: [gmx-users] using two different combination rules for the LJ potentia

Ana West wrote: Thank you so much for the kind reply. I made a mistake in my previous posting - I am dealing with combination rule 1 and the combination rule 2. Initially I converted the parameters according to section 5.3.3 of the manual and when I did some tests to verify my force-field, the

[gmx-users] (no subject)

So sorry! You're absolutely right. Re the question on Zn 2+ I am asking about the ffgmx forcefield. Marc Charendoff wrote: > Hello, > >        I am curious - is there anyway to see what assumptions were made when >parameterizing the Zn 2+ ion? Was it tetrahedrally or octahedrally >coordin

[gmx-users] Wrong pressure with "mdrun -rerun" option

Hello all, >From the notes for gmx 4.0.5, the pressure and virial from "-rerun" should be >correct. However, I did a test for a box of tip3p water and found the pressure >results from rerun were different compared to the original results. For the >first MD simulation , I simulated it for 200 ps

Re: [gmx-users] (no subject)

Marc Charendoff wrote: So sorry! You're absolutely right. Re the question on Zn 2+ I am asking about the ffgmx forcefield. I don't believe the answers to your questions are in the public domain, for several reasons. First, ffgmx is an old, deprecated force field that is somewhat of a

RE: [gmx-users] genconf

Hi Justin, I checked the trjconv help. It also takes .gro files. If so, do I still need to provide a .tpr file? (if yes, then the output can be .gro?) Payman -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: J

Re: [gmx-users] genconf

Payman Pirzadeh wrote: Hi Justin, I checked the trjconv help. It also takes .gro files. If so, do I still need to provide a .tpr file? (if yes, then the output can be .gro?) Any of the listed file formats can be input or output. To fix "broken" molecules, you must supply a .tpr file. If y

Re: [gmx-users] Wrong pressure with "mdrun -rerun" option

LuLanyuan wrote: > Hello all, >>From the notes for gmx 4.0.5, the pressure and virial from "-rerun" should be >>correct. However, I did a test for a box of tip3p water and found the >>pressure results from rerun were different compared to the original results. >>For the first MD simulation , I s

Re: [gmx-users] Wrong pressure with "mdrun -rerun" option

Hi Mark, Thanks for your reply. Yes, I did save velocities in the same frequency as positions. And the length of two compared trajectories are exactly the same. I think I've figured it out and I did looked at the average values as the output of the g_energy. It seems the number 545.384 from the

[gmx-users] Error in hdb file ffG43a1p.hdb

Hi, i am trying to run md for protein-peptide complex. the peptide has phosphorylated tyrosine. i got the following error when i run pdb2gmx Fatal error: Error in hdb file ffG43a1p.hdb: Wrong number of control atoms (2 iso 3) on line: 11N-CCA I would greatly appreciate if s

Re: [gmx-users] Wrong pressure with "mdrun -rerun" option

Lanyuan Lu wrote: > Hi Mark, > Thanks for your reply. Yes, I did save velocities in the same frequency > as positions. And the length of two compared trajectories are exactly > the same. I think I've figured it out and I did looked at the average > values as the output of the g_energy. It seems

Re: [gmx-users] Error in hdb file ffG43a1p.hdb

Thamu wrote: Hi, i am trying to run md for protein-peptide complex. the peptide has phosphorylated tyrosine. i got the following error when i run pdb2gmx Fatal error: Error in hdb file ffG43a1p.hdb: Wrong number of control atoms (2 iso 3) on line: 11N-CCA I would greatly