[gmx-users] problem with mpiexec, mdrun in gromacs/4.0.7

Hello I want to run a simulation in gromacs/4.0.7 because this version supports v-rescale option for thermostat and I need that. tcoupl=v-rescale   in this version the grompp command does not need -np option. please let me know how I can specify the number of processors for my job.   I use a .ll

Re: [gmx-users] rationale behind tcoupling ligand with protein instead of with SOL

On 2011-04-11 01:24:49AM -0500, Mark Abraham wrote: > > Any rationale behind the thermostat coupling of a ligand with the protein > > instead of the ligand with the solvent (as shown in Justin's T4 Lysozyme > > binding example)? Especially with small drug-type molecules as generally the > > ligand

Re: [gmx-users] problem with mpiexec, mdrun in gromacs/4.0.7

Hello I want to run a simulation in gromacs/4.0.7 because this version supports v-rescale option for thermostat and I need that. tcoupl=v-rescale Do the job properly, and install 4.5.4 for better parallel performance and more bug fixes. *in this version the grompp command does not need -np

Re: [gmx-users] rationale behind tcoupling ligand with protein instead of with SOL

On 2011-04-11 01:24:49AM -0500, Mark Abraham wrote: Any rationale behind the thermostat coupling of a ligand with the protein instead of the ligand with the solvent (as shown in Justin's T4 Lysozyme binding example)? Especially with small drug-type molecules as generally the ligand might/would ta

[gmx-users] Re : Simulation for prediction of binding between a peptide and protein

Hi, I want to know how can I predict where a designed peptide will bind to my protein target or not using simulation ... Can anybody guide me ?? -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan Na

Re: [gmx-users] comm-grps for a membrane-protein-ligand system

Peter C. Lai wrote: Should I couple a ligand associated with a membrane protein to the same COM group as the Protein_POPC group? It makes sense to me that would be the case since if we are investigating the interaction between protein+membrane and ligand we want to have the same COM correctio

Re: [gmx-users] Re : Simulation for prediction of binding between a peptide and protein

Hi, I want to know how can I predict where a designed peptide will bind to my protein target or not using simulation ... Can anybody guide me ?? I don't think anybody has the computational resources to answer this question with unguided MD. Docking programs are probably the way to get a guid

[gmx-users] mdrun segmentation fault

Hello gmx users, My system for NVT equilbration runs into segmentation fault as soon as I try to run it. It does not give any warning or hint of what might be going wrong. Since I am a new user I am having difficulty exploring the plausible reasons. System: Protein( polyhistidine), 20 2,5-dihydr

Re: [gmx-users] mdrun segmentation fault

shivangi nangia wrote: Hello gmx users, My system for NVT equilbration runs into segmentation fault as soon as I try to run it. It does not give any warning or hint of what might be going wrong. Since I am a new user I am having difficulty exploring the plausible reasons. System: Protein(

[gmx-users] g_hbond

Hello, I am trying to calculate number of hydrogen bond (O-H---CL)in my system. I use the following command g_hbond -f 3.trr -s 3.tpr -n hbond18.ndx -nonitacc -num Output file hbnum.xvg shows zero number of hydorgen bond. Can you tell me why its showing zero no. A strong peak is found in r

Re: [gmx-users] g_hbond

Nilesh Dhumal wrote: Hello, I am trying to calculate number of hydrogen bond (O-H---CL)in my system. I use the following command g_hbond -f 3.trr -s 3.tpr -n hbond18.ndx -nonitacc -num Output file hbnum.xvg shows zero number of hydorgen bond. Can you tell me why its showing zero no. A

Re: [gmx-users] g_hbond

Is there any way to specify clorin and florin atoms as a receptor. Nilesh On Mon, April 11, 2011 11:08 am, Justin A. Lemkul wrote: > > > Nilesh Dhumal wrote: > >> Hello, >> >> >> I am trying to calculate number of hydrogen bond (O-H---CL)in my >> system. >> >> I use the following command >> >> >

Re: [gmx-users] g_hbond

Nilesh Dhumal wrote: Is there any way to specify clorin and florin atoms as a receptor. Modify the code. -Justin Nilesh On Mon, April 11, 2011 11:08 am, Justin A. Lemkul wrote: Nilesh Dhumal wrote: Hello, I am trying to calculate number of hydrogen bond (O-H---CL)in my system. I u

[gmx-users] rationale behind tcoupling ligand with protein instead of with SOL

You didn't state your usage, but if you're doing US or decoupling, etc (some method where you lose the dynamics anyway) I suggest that you use Langevin dynamics. You will get the correct ensemble. Separate temperature coupling groups is a trick that helps in some cases, but it still does no

Re: [gmx-users] comm-grps for a membrane-protein-ligand system

Ok thanks My primary concern is to cancel membrane-protein drift - the protein getting pushed to one side of the membrane box (also it's important for me to have the protein stay centered in the box too). I have not seen stability issues otherwise with COM turned on in the case of the unbound pr

[gmx-users] How to install GROMACS in Rocks Cluster 4.5.4 : ERROR

Dear community. I have been trying to install gromacs 4.5.4 in my rocks cluster version 5.4 but unfortunately the system showed "configure: error: Cannot find fftw3 library" after launch the ./configure (you can see below) Really I do not understand because I did before this: # export LDFLAGS="-

Re: [gmx-users] comm-grps for a membrane-protein-ligand system

Peter C. Lai wrote: Ok thanks My primary concern is to cancel membrane-protein drift - the protein getting pushed to one side of the membrane box (also it's important for me to have the protein stay centered in the box too). I have not seen There is no "center" to a periodic system. Molecu

Re: [gmx-users] How to install GROMACS in Rocks Cluster 4.5.4 : ERROR

Miguel Quiliano Meza wrote: Dear community. I have been trying to install gromacs 4.5.4 in my rocks cluster version 5.4 but unfortunately the system showed "configure: error: Cannot find fftw3 library" after launch the ./configure (you can see below) Really I do not understand because I di

Re: [gmx-users] g_hbond

Try the -contact option. Erik Nilesh Dhumal skrev 2011-04-11 17.12: Is there any way to specify clorin and florin atoms as a receptor. Nilesh On Mon, April 11, 2011 11:08 am, Justin A. Lemkul wrote: Nilesh Dhumal wrote: Hello, I am trying to calculate number of hydrogen bond (O-H---CL)i

[gmx-users] Pressure coupling problem

Hi, I'm still in my first few months of using Gromacs. I started by creating an *.itp and *.top file for *Ethanol* using CHARMM force field parameters. I made the molecule and it looked fine, put 1000 molecules in a box, energy minimized it to a negative potential energy, viewed it on VMD, again

Re: [gmx-users] Re : Simulation for prediction of binding between a peptide and protein

You can try Rosetta for flexible peptide docking. On 11 April 2011 15:32, Mark Abraham wrote: > Hi, >> >> I want to know how can I predict where a designed peptide will bind to my >> protein target or not using simulation ... Can anybody guide me ?? >> > > I don't think anybody has the computat

Re: [gmx-users] g_hbond

Is it possible to find number of hydrogen bonds using g_hbond by considering the distance between Acceptor-hydrogen instead of the distance between Acceptor-Donor atoms. Nilesh On Mon, April 11, 2011 3:32 pm, Erik Marklund wrote: > Try the -contact option. > > > Erik > > > > Nilesh Dhumal skrev 2

Re: [gmx-users] Pressure coupling problem

Fabian Casteblanco wrote: Hi, I'm still in my first few months of using Gromacs. I started by creating an *.itp and *.top file for /Ethanol/ using CHARMM force field parameters. I made the molecule and it looked fine, put 1000 molecules in a box, energy minimized it to a negative potenti

[gmx-users] Pressure coupling problem

Hi, I'm still in my first few months of using Gromacs.  I started by creating an *.itp and *.top file for Ethanol using CHARMM force field parameters.  I made the molecule and it looked fine, put 1000 molecules in a box, energy minimized it to a negative potential energy, viewed it on VMD, again l

[gmx-users] Re: gmx-users Digest, Vol 84, Issue 90

gt; > > > On Mon, April 11, 2011 11:08 am, Justin A. Lemkul wrote: > >> Nilesh Dhumal wrote: > >> > >>> Hello, > >>> > >>> > >>> I am trying to calculate number of hydrogen bond (O-H---CL)in my > >>> system. > >&g

Re: [gmx-users] Pressure coupling problem

So your density graph looks stabilized? I also tend to look for changes in box x, y, z as well since the scale of their changes is easier to track. Sometimes it helps to look at the error vs. rmsd vs total drift statistics as well for such parameters that are easier to track - again if density sh

Re: [gmx-users] How to install GROMACS in Rocks Cluster 4.5.4 : ERROR

1. Please do not reply to the entire digest. It confuses the archive. 2. Please heed the following message from your digest: When replying, please edit your Subject line so it is more specific than "Re: Contents of gmx-users digest..." Miguel Quiliano Meza wrote: Dear community. Thank you fo

Re: [gmx-users] g_hbond

When running g_hbond -h, I see the following, among other things: -[no]da bool yes Use distance Donor-Acceptor (if TRUE) or Hydrogen-Acceptor (FALSE) Hope that helps. Erik Nilesh Dhumal skrev 2011-04-11 23.05: Is it possible to find number of hydrogen bo

[gmx-users] g_saltbr

Hi, I am curious how the donor and acceptor atoms are picked with g_saltbr. For examples, with Asp, it picked CG instead of the two ODs, and with LYS, it picked  CE instead of NZ. Why? Thanks for your help in advance. Simon Sham -- gmx-users mailing listgmx-users@gromacs.org http://lists.gr

Re: [gmx-users] g_saltbr

simon sham wrote: Hi, I am curious how the donor and acceptor atoms are picked with g_saltbr. For examples, with Asp, it picked CG instead of the two ODs, and with LYS, it picked CE instead of NZ. Why? g_saltbr does its searching based on charge groups. Looks like its deciding its label

Re: [gmx-users] Re : Simulation for prediction of binding between a peptide and protein

but using docking I have to fix the grid and have to dock at that position... which is not my objective ... I want the peptide to come and bind own its own to the protein... I have heard of full body dock , in which there is no need to define grid points , will that be useful ?? On Mon, Apr 11, 2

[gmx-users] Acpype error

Hi GMX users, When I ran acpype.py on my computer, I got one error like this: File "./acpype.py", line 67, in from datetime import datetime ImportError: No module named datetime I use Python-2.6.6, I do not know how this error happen, could someone help me figure it out? Thanks very much in a

Re: [gmx-users] g_hbond

I tried to use contact and -da together with following command g_hbond -f 3.trr -s 3.tpr -n hbond19.ndx -nonitacc -noda -r 0.5 -contact -num I am getting following error. Fatal error:Can not analyze contact between H and A: turn off -noda Nilesh On Mon, April 11, 2011 5:05 pm, Nilesh

Re: [gmx-users] multicomponent system- units

Hello Mark, Thank you for your reply. I have already created the energy groups. I am trying to validate pairwise energy values (nonbonded) with some other work ( a thermodynamic model) where they fit these AA AB BB (E_AA, E_AB, E_BB) energies so that some phase diagrams are reproduced. The pairwis

Re: [gmx-users] Acpype error

Dear Qinghua Liao, Could you give a little more information about your problem? How you ran the program? "./acpype -i "your_ligand_file.pdb" or what? Did you tested the installation? (At folder acpype/test) Does acpype properly installed? Does Ambertools properly installed? Best regards,

[gmx-users] orientational relaxation

dear users how can i make a orientational relaxation without traslation of molecules center of mass thanks in advances  -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/M

Re: [gmx-users] multicomponent system- units

Hello Mark, Thank you for your reply. I have already created the energy groups. I am trying to validate pairwise energy values (nonbonded) with some other work ( a thermodynamic model) where they fit these AA AB BB (E_AA, E_AB, E_BB) energies so that some phase diagrams are reproduced. The pa

Re: [gmx-users] orientational relaxation

dear users how can i make a orientational relaxation without traslation of molecules center of mass thanks in advances Position restraints? Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www

[gmx-users] Unexpected results arising from T- and P-coupling methods

Dear gmxers, According to my recent practice, we find that the Berensen methods for T- and P- coupling can yield reasonable averaged density as a function of temperature, but when the v-rescale method and the Parrinello-Rahman method are employed for T- and P- coupling, somewhat unexpected re

Re: [gmx-users] orientational relaxation

yes , position restraints of molecules that only allow to orient. regards. --- On Mon, 4/11/11, Mark Abraham wrote: From: Mark Abraham Subject: Re: [gmx-users] orientational relaxation To: "Discussion list for GROMACS users" Date: Monday, April 11, 2011, 9:10 PM

Re: [gmx-users] orientational relaxation

yes , position restraints of molecules that only allow to orient. What's your question? Most tutorials will use position restraints at some stage. There's theory discussion in the manual. Mark regards. --- On *Mon, 4/11/11, Mark Abraham //* wrote: From: Mark Abraham Subject: R

Re: [gmx-users] orientational relaxation

Hi Daniel, If you want to fix the com position, specify the molecule as comm-grps. If you really don't want movement of the com, and use pressure coupling, first put the molecule at the origin. Hope it helps, Tsjerk On Apr 12, 2011 7:28 AM, "Mark Abraham" wrote: > yes , position restraints of

[gmx-users] re: Acpype error

Dear Prof. Aldo Segura-Cabrera, Thanks very much for your reply. I just download the package of Acpype, and I ran ../acpype.py -i FFF.pdb to test acpype.py, but then I got the error. Amber11 and AmberTools 1.4 have been successfully installed on the computer. I have read the installation instruc