[gmx-users] Re: How to set the density of the box?

>>       Hello, I want to set the density of the box (e.g. set 1 g/ml for >> the water box). I use the density option in the editconf, then use the >> genbox to generate the box, but the result of the density is not what I >> setted. How can  I do ? It seems to be much easier in your case to calcu

[gmx-users] Time for equilibration

Hello All, I have a protein of 576 amino acid long, and has a barell shape topolgy. I have done MD simulation on it for 1ns, and my protein has got distorted shape, i.e, one of the strand became coil and other strands became small. I wrote this query before also, can it be possible that this is du

Re: [gmx-users] OpenMM

The two tables was the averages generated by the serial code and by the parallel code (I have used, as you suggest me, the option rerun of mdrun on the CPU to analyze the energies obtained with the parallel simulation on GPU)...Could you tell me if these results could be correct and why? I h

Re: [gmx-users] modifying source code

On 15/04/2010 12:32 PM, Sang-Won Park wrote: Hello all, I am trying to modify the source code. My simulation system consists of several huge modecules disolved in a liquid. The relative orientation among the huge molecules is not significant in the system, and I concern structural properties onl

[gmx-users] modifying source code

Hello all, I am trying to modify the source code. My simulation system consists of several huge modecules disolved in a liquid. The relative orientation among the huge molecules is not significant in the system, and I concern structural properties only, not dynamic properties, in the equil

[gmx-users] how to calculate diffusion constant of the entire lipid-bilayer

Hi, I was interested in calculating the diffusion constant of the center of mass of entire lipid-bilayer ( not individual lipid molecules). Regarding this, I had two doubts I wanted to clarify: 1. Since I am interested in calculating the diffusion constant of the bilayer iteself, I guess

[gmx-users] Concerns with g_wham

Hello, I have been using g_wham, but I have a few questions that I can't find answers to online. When using WHAM, one does not need the forces between the pull groups to calculate the PMF, yet g_wham won't run without it. Is there a reason for this? Also, when using the pull code, I am allowed

Re: [gmx-users] OpenMM

On 14/04/2010 7:10 PM, PACIELLO GIULIA wrote: Well, I have used the option -rerun to 'rerun' on CPU the simulation from the parallel code. As you can see in the following tables, results are very similar for non bonded terms, but not for the other energetic terms (these are avereges obtained from

Re: [gmx-users] How to set the density of the box?

kecy...@sina.com wrote: Hello, I want to set the density of the box (e.g. set 1 g/ml for the water box). I use the density option in the editconf, then use the genbox to generate the box, but the result of the density is not what I setted. How can I do ? The density of the box will

[gmx-users] How to set the density of the box?

  Hello, I want to set the density of the box (e.g. set 1 g/ml for the water box). I use the density option in the editconf, then use the genbox to generate the box, but the result of the density is not what I setted. How can  I do ?   I have another question, I don't find the tip3p.gro

Re: [gmx-users] nstfout parameter

Bharath.K. Chakravarthi wrote: hi .. in my *.mdp file one parameter named mstfout is set to 0 can you please tell me the use of this parameter Please see the manual, section 7.3.8. -Justin -- Bharath.K.Chakravarthi Ph:9535629260 -- Justin

[gmx-users] nstfout parameter

hi .. in my *.mdp file one parameter named mstfout is set to 0 can you please tell me the use of this parameter -- Bharath.K.Chakravarthi Ph:9535629260 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://w

Re: [gmx-users] *.xtc file is not getting created by mdrun program :(

Thank you very much for your replay sir... On Wed, Apr 14, 2010 at 5:36 AM, Justin A. Lemkul wrote: > > > Bharath.K. Chakravarthi wrote: > >> sir should i set dat to 0 or what to do >> >> > I clearly stated that you should set nstxtcout > 0 in my first message. > Leaving any output control

Re: [gmx-users] *.xtc file is not getting created by mdrun program :(

Bharath.K. Chakravarthi wrote: sir should i set dat to 0 or what to do I clearly stated that you should set nstxtcout > 0 in my first message. Leaving any output control parameter set to zero means "produce output every zero steps" or essentially, not at all. -Justin On Wed, Apr

Re: [gmx-users] *.xtc file is not getting created by mdrun program :(

sir should i set dat to 0 or what to do On Wed, Apr 14, 2010 at 5:32 AM, Bharath.K. Chakravarthi < bharath.chakravar...@gmail.com> wrote: > > > On Wed, Apr 14, 2010 at 5:31 AM, Bharath.K. Chakravarthi < > bharath.chakravar...@gmail.com> wrote: > >> Thank you for your kind replay sir >> s

Re: [gmx-users] *.xtc file is not getting created by mdrun program :(

Bharath.K. Chakravarthi wrote: Thank you for your kind replay sir sir in my .mdp file there is nstxtout instead of nstxtcout sir and it is set to 500 is this what u told... No, this is not what I said. These are different settings entirely. nstxout is for the .trr file, nstxtcout is

Re: [gmx-users] *.xtc file is not getting created by mdrun program :(

Thank you for your kind replay sir sir in my .mdp file there is nstxtout instead of nstxtcout sir and it is set to 500 is this what u told... i have also attached the .mdp file in this mail sir On Wed, Apr 14, 2010 at 5:18 AM, Justin A. Lemkul wrote: > > > Bharath.K. Chakravarthi wrote: > >>

Re: [gmx-users] *.xtc file is not getting created by mdrun program :(

On Wed, Apr 14, 2010 at 5:31 AM, Bharath.K. Chakravarthi < bharath.chakravar...@gmail.com> wrote: > Thank you for your kind replay sir > sir in my .mdp file there is nstxtout instead of nstxtcout sir and it is > set to 500 > is this what u told... > i have also attached the .mdp file in this m

Re: [gmx-users] *.xtc file is not getting created by mdrun program :(

Bharath.K. Chakravarthi wrote: hi there i tried to run MD and i wanted to use *.xtc file in vmd to visualize the protein but unfortunately there is no such file i given the command like this mdrun -nice 0 -v -s input3.tpr -o md_traj.trr -x md_traj.xtc -c md_final.gro -e md_ener.edr as proce

[gmx-users] *.xtc file is not getting created by mdrun program :(

hi there i tried to run MD and i wanted to use *.xtc file in vmd to visualize the protein but unfortunately there is no such file i given the command like this mdrun -nice 0 -v -s input3.tpr -o md_traj.trr -x md_traj.xtc -c md_final.gro -e md_ener.edr as procedure this should create md_traj.xtc fil

Re: [gmx-users] Hydrogens missing during parameterization

Well, ffG43a2 is a GROMOS FF too! So look at the topology and you'll see that it also misses some NON_POLAR hydrogens. You probably generated you itp file using pdb2gmx and got a gro file with it. Then the absence of H did not appear! The H that are involved in H-bonding are explicitly rep

Re: [gmx-users] Hydrogens missing during parameterization

Anirban Ghosh wrote: Hi XAvier, Thanks for the reply. Actually I want to use this ligand with a protein and run the complex using ffG43a2 force-field of GROMACS4.0.7. So is it correct to leave away those 3 hydrogens HA, HB1 and HB2, which are not explicitly described? Because in protein-lig

Re: [gmx-users] Hydrogens missing during parameterization

Hi XAvier, Thanks for the reply. Actually I want to use this ligand with a protein and run the complex using ffG43a2 force-field of GROMACS4.0.7. So is it correct to leave away those 3 hydrogens HA, HB1 and HB2, which are not explicitly described? Because in protein-ligand complexes, hydrogen bond

Re: [gmx-users] Hydrogens missing during parameterization

You have the proper itp file for the GROMOS FF. Some H are not explicitly described! On Apr 14, 2010, at 12:05 PM, Anirban Ghosh wrote: Hi, XAvier, Sorry for that mistake. Yes, exactly PRODRG is not giving the non- polar hydrogens. There I am using the GROMOS96.1 FF. So is there any way

Re: [gmx-users] Hydrogens missing during parameterization

Hi, XAvier, Sorry for that mistake. Yes, exactly PRODRG is not giving the non-polar hydrogens. There I am using the GROMOS96.1 FF. So is there any way to get the proper .itp file? I mean any other online server like PRODRG? Or How can I derive the proper .itp file manually? Any suggestion is welco

Re: [gmx-users] Hydrogens missing during parameterization

You are missing HB1 and HB2, not HB2 and HB3 :)) This is due to the force field our are using. Gromos I presume: it uses the united H idea: non-polar H are not explicitly modeled. you should be able to erase those from your gro file, but I would suggest you get into some literature about the FF

[gmx-users] Hydrogens missing during parameterization

Hi ALL, I have a ligand LDOPA with 25 atoms (including all hydrogens).: --- DAH COORDS 25 1DAH O1 5.988 5.216 9.128 1DAH C2 5

Re: [gmx-users] OpenMM

Well, I have used the option -rerun to 'rerun' on CPU the simulation from the parallel code. As you can see in the following tables, results are very similar for non bonded terms, but not for the other energetic terms (these are avereges obtained from g_energy): PARALLEL CODE Angle: 4256

Re: [gmx-users] OpenMM

On 14/04/2010 5:18 PM, PACIELLO GIULIA wrote: I dont'know if this is the right way to test that things converge to the same value...but I have made an energy minimization on CPU of the two output (parallel and serial). I have obtained this results: FROM PARALLEL OUTPUT Potential Energy = -1.6960

[gmx-users] Re: small help

Again, it is better to post these question on the gromacs list. You'll find more people able to help you and the exchange might be profitable to others. I am not sure what you want to do! Please explain what you want to do and what has failed to give you the answer you are looking for. XAvier.

Re: [gmx-users] OpenMM

I dont'know if this is the right way to test that things converge to the same value...but I have made an energy minimization on CPU of the two output (parallel and serial). I have obtained this results: FROM PARALLEL OUTPUT Potential Energy = -1.6960029e+04 Maximum force = 1.7282695e+03