[gmx-users] high temperature during mdrun

-equilibrium MD stuff freezegrps    = slab freezedim = Y Y Y Can anyone help me to solve this problem?thank you in advance Fatemeh Ramezani -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting

[gmx-users] mdrun failure

freezegrps    = slab freezedim = Y Y Y Can anyone help me to solve this problem?thank you in advance Fatemeh Ramezani -- 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 http

[gmx-users] mdrun failed

to coupleseparately tc-grps =ProteinNon-Protein ; Time constant (ps) andreference temperature (K) tau-t   = 0.2 0.2 ref-t   = 310 310   ; Non-equilibrium MDstuff freezegrps  = slab freezedim   = Y Y Y   Fatemeh Ramezani

[gmx-users] Fw: mdrun failure

md3.edr to ./#md3.edr.20#starting mdrun 'Proteinin water'10 steps,   100.0 ps. Can you help me toprevent from mdrun failing?Thank you very much   Fatemeh Ramezani -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List be

[gmx-users] mdrun failure

.trr to ./#fws_md3.trr.20#  Back Off! I just backedup traj_comp.xtc to ./#traj_comp.xtc.22#  Back Off! I just backedup md3.edr to ./#md3.edr.20# starting mdrun 'Proteinin water' 10 steps,   100.0 ps.  Can you help me toprevent from mdrun failing? Thank you very much    Fatemeh Rame

[gmx-users] lincs warning

Dear gmx usersplease help me if you know how can I change lincs warning threshold in mdp file or in command? thank you Fatemeh Ramezani -- 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

[gmx-users] Fw: lincs warnin threshold

 Fatemeh Ramezani On Sunday, 12 March 2017, 20:16, fatemeh ramezani <fr_...@yahoo.com> wrote: Hi I have a system of protein-gold-ions-water to simulate. The force field which I use, is Golp-charmm. In this force field two au atoms with mass 0.5 and charge 0.3 (AUC) rotates

[gmx-users] lincs warnin threshold

Hi I have a system of protein-gold-ions-water to simulate. The force field which I use, is Golp-charmm. In this force field two au atoms with mass 0.5 and charge 0.3 (AUC) rotates around the main au atoms (with mass 196.967 and charge -0.3: AUS)that are freezed during the simulation. from the

[gmx-users] free energy

be considered so that the total simulation time of lambdas be 8 ns? I hope I could correctly ask my question. I would greatly appreciate your response to my question.  Fatemeh Ramezani -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List

[gmx-users] adding new residue

appeared:number of coordinates in coordinate file (x.pdb, 72323) does not match topology (x.top, 95870) that the difference is equal to sol atom number that is 23547I dont know how can I solve this problem. I appreciate any help.  Fatemeh Ramezani -- Gromacs Users mailing list * Please

[gmx-users] Fw: Add new residue to oplsaa force field

mktop doesn't produce these dihedral coefficient? and how can I solve it?Thanks in advance Fatemeh Ramezani -- 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 http

[gmx-users] Add new residue to oplsaa force field

this problem?Thanks for your guides Fatemeh Ramezani -- 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 http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https

[gmx-users] Add new residue to forcefield

In topol.top line 258 contain atoms 25 23 27 that are atoms OH CG CD and I added the angle between them in [angletypes] section in ffbonded.itp file. I would be grateful if anyone could shed some light on the origin of this error, and on what I can do to correct it.   Fatemeh Ramezani

[gmx-users] graphene top file

1.42e-01 4.00e+05 1011 1 1.42e-01 4.00e+05 1.42e-01 4.00e+05 1112 1 1.42e-01 4.00e+05 1.42e-01 4.00e+05 Fatemeh Ramezani -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support

[gmx-users] In itp file from prodrg, what is C0 and C1 in bonds, angles and dihedrals section

Hi Dear gmx-users In itp file from prodrg, what is C0 and C1 in bonds, angles and dihedrals section; [ bonds ] ; ai aj fuc0, c1, ... [ angles ] ; ai aj ak fuc0, c1, ... [ dihedrals ] ; ai aj ak al fuc0, c1, m, ... Thank you Fatemeh Ramezani -- Gromacs Users mailing

[gmx-users] boron atom parameter

build a top file for this ligand? regards Fatemeh Ramezani -- 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 http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests

[gmx-users] (no subject)

Dear Users I run this command:  nohup  mpirun -np 8  mdrun_mpi  -s x.tpr -o x.trr -c x.pdb -g x.log -e x.edr   Despite the use of nohup and , mdrun will stop after closing the putty window. Can anyone help me to solve this problem?   thank you in advance -- Gromacs Users mailing list *

[gmx-users] Mdrun kill despite the use of nohup

Dear Users I run this command:  nohup  mpirun -np 8  mdrun_mpi  -s x.tpr -o x.trr -c x.pdb -g x.log -e x.edr   Despite the use of nohup and , mdrun will stop after closing the putty window. Can anyone help me to solve this problem?   thank you in advance -- Gromacs Users mailing list *

[gmx-users] aptamer

?   Fatemeh Ramezani -- 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 http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman

[gmx-users] Is viscosity increasing in the system due to the protein unfolding?

the simulation. Due to the fact that by unfolding of protein its viscosity increase, can I relate the viscosity arising to the unfolding of protein? Fatemeh Ramezani -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting