[gmx-users] angle restraints

hello I want to add angle restraints in my itp file for a ligand. what is the proper way of inserting angle restraint in .itp file ? Is there any keywords I have to add to my .mdp file for angle restraints? I have searched the mail archieve, I found many things about adding dihedral angle restra

Re: [gmx-users] g_dipoles, average not the same as from g_analyze

Dear Emanuel, Please, check http://lists.gromacs.org/pipermail/gmx-users/2010-March/049316.html and Berk reply. I did never use -av (-a ?) option, maybe there is similar bug in average.xvg. Anyway last column of Mtot.xvg gives really correct norm of M_tot vector! Regards, Dmitri -

Re: [gmx-users] structure file long chains

Moeed wrote: I dont know if the hdb file is correct. Actually I want to learn how it works. The .hdb file works. I've used it :) Did you try it yourself with the examples posted? 1- Manual says the third columns are name of new H atoms (here, H1, H2). why are they not the same as th

[gmx-users] structure file long chains

I dont know if the hdb file is correct. Actually I want to learn how it works. 1- Manual says the third columns are name of new H atoms (here, H1, H2). why are they not the same as those in rtp file (H11, H12). There is no H1 and H2 in rtp file ( http://lists.gromacs.org/pipermail/gmx-users/2009-M

[gmx-users] g_dipoles, average not the same as from g_analyze

Dear gromacs users, Sorry but my last email was not correct. I have following question: With the use of the g_dipoles tool I have analysed the average dipole moment using following command: g_dipoles -f *.trr -s *.tpr -n *.ndx -av average.xvg I think the option -av calculates the average of

[gmx-users] g_dipoles, average not the same as from g_analyze

Dear gromacs users, I have following question: With the use of the g_dipoles tool I have analysed the average dipole moment using following command: g_dipoles -f *.trr -s *.tpr -n *.ndx -av average.xvg I think the option -av calculates the average of the dipole moment of the system I have ch

[gmx-users] converting amber parameter to OPLS

Dear all: I'm considering to convert the ATP/ADP parameters from amber (http://www.pharmacy.manchester.ac.uk/bryce/amber ) into OPLS format. My question is, have you guys done similar things? If so, can you give me some information on what kind of thing I should be aware of? Like the scaling

Re: [gmx-users] field-specified name for sulfate

shiva birgani wrote: Hi All I am trying to add sodium sulfate to the system but I receive this fetal error Fatal error: No such moleculetype SO4 Could anybody tell me what is the force field-specified name of sulfate ion in OPLS-AA/L all-atom force field? Rather than implicating

Re: [gmx-users] Re: Simulation with CsCl

Dear Sonali, Unfortunately development of force-field parameters is difficult, and even more so for bivalent ions and transition metals. This is certainly not suitable as a project to begin with. Having said that, a careful search in the literature will reveal that many sets of parameters for met

Re: [gmx-users] Re: Simulation with CsCl

sonali dhindwal wrote: Hello All , I am also trying to simulate my protein with Mn ion present in it. So can I create the topology entry for Mn ion similar to MG2+ ion ? and how can I get the values of C6 and C12 leonard jones potential in [atom type] entry and will it be required to add [no

Re: [gmx-users] tracking the time for an md run

Rabab Toubar wrote: Hi, Can anyone let me know how to know how long the md run would take, or how long is left. I tried tailing it, but couldn't find a time factor there If you use mdrun -v, it will print a completion estimate as it goes along. -Justin Thanks Rabab -- =

[gmx-users] field-specified name for sulfate

Hi All I am trying to add sodium sulfate to the system but I receive this fetal error Fatal error: No such moleculetype SO4 Could anybody tell me what is the force field-specified name of sulfate ion in OPLS-AA/L all-atom force field? regards, Shiva -- gmx-users mailing listgmx-users@groma

Re[6]: [gmx-users] Non-conservation of total energy while using structure file to resume the simulation

Hi, Tsjerk. Thanks for your help. > Try > editconf -f your_run_input_file.tpr -o test.gro > to see if the box is stored correctly in the .tpr. Alternatively, you > can do gmxdump -s your_run_input_file.tpr, and browse for the box in > the output. Yea, both tests show "zero" box right in .tpr f

[gmx-users] tracking the time for an md run

Hi, Can anyone let me know how to know how long the md run would take, or how long is left. I tried tailing it, but couldn't find a time factor there Thanks Rabab -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the ar

Re: [gmx-users] Re: Simulation with CsCl

Hello All , I am also trying to simulate my protein with Mn ion present in it. So can I create the topology entry for Mn ion similar  to MG2+ ion ? and how can I get the values of C6 and C12 leonard jones potential in [atom type] entry and will it be required to add [nonbond_params] also ? how c

Re: Re[4]: [gmx-users] Non-conservation of total energy while using structure file to resume the simulation

Hi Dmitri, Try editconf -f your_run_input_file.tpr -o test.gro to see if the box is stored correctly in the .tpr. Alternatively, you can do gmxdump -s your_run_input_file.tpr, and browse for the box in the output. Then, see if you can reproduce the problem with the last frame of the .trr file ex