Re: [gmx-users] PRODRG

9, 2011 at 9:42 AM jorge_quint...@ciencias.uis.edu.co wrote: >> >> > I think that is better to use antechamber tools. >> > >> > >> > > On 10/02/2011 3:40 AM, mohsen ramezanpour wrote: >> > >> Dear Users >> > >> >> > >>

Re: [gmx-users] PRODRG

tin A. Lemkul wrote: > > > mohsen ramezanpour wrote: > >> Dear Dr.Justin >> >> I have read this section before. >> There are 2 problem: >> 1:ADDHYD atomname and DELHYD atomname commands dosen't work! >> they result in ERROR in PRODRG >>

[gmx-users] Active site

Dear All I want to evaluate the binding free energy of protein-dryg. My protein has so many atoms(5000 atoms),it make running too long. I want to use Umbrella sampling for this. Can I separate active site of protein (a radious of 3 nm around of my drug )and do my work on this system? Thanks in a

Re: [gmx-users] Active site

nt to learn how I can do this. Thanks in advance for your guidance On Sat, Feb 12, 2011 at 4:50 PM, Justin A. Lemkul wrote: > > > mohsen ramezanpour wrote: > >> Dear All >> >> I want to evaluate the binding free energy of protein-dryg. >> >> My protein ha

Re: [gmx-users] Active site

me know if there are any other Thanks in advance for your reply On Sun, Feb 13, 2011 at 3:55 PM, Justin A. Lemkul wrote: > > > mohsen ramezanpour wrote: > >> Dear Dr.Justin >> >> I couldn't find any tutorial for doing free energy cycles with gromacs. >

[gmx-users] membrane-protein tutorial

Dear all I am doing Membrane -protein tutorial. Actually I did each step carefully,I could score down my lipids 26 times. But there were two problems: 1-I get ~77 A for area per lipid in 26th step not 71 as Dr.Justin has said 2-I tried to do more iteration to make closer my area per lipid to 71,Bu

Re: [gmx-users] membrane-protein tutorial

for your reply On Mon, Mar 7, 2011 at 5:42 PM, Justin A. Lemkul wrote: > > > mohsen ramezanpour wrote: > >> Dear all >> >> I am doing Membrane -protein tutorial. >> Actually I did each step carefully,I could score down my lipids 26 times. >> But the

Re: [gmx-users] membrane-protein tutorial

iteration. In the other words it seems it dosen't converge!! What do you think? Thanks in advance On Mon, Mar 7, 2011 at 6:09 PM, Justin A. Lemkul wrote: > > > mohsen ramezanpour wrote: > >> Dear Dr.Justin >> Yes,I know,it deleted some lipids according to inflateGRO scri

Re: [gmx-users] membrane-protein tutorial

Ok.Thank you very much On Mon, Mar 7, 2011 at 6:29 PM, Justin A. Lemkul wrote: > > > mohsen ramezanpour wrote: > >> Dear Dr.justin >> Thank you.You are right. >> I did what you said. >> >> please let me know the answer of my other question in first e

[gmx-users] Membrane-protein tutorial

Dear Dr.Justin Is there any criteria for choosing vdwradii for carbon atoms? Because I have changed it from 0.15 to 0.375,but there were afew water molecules,it is difficult to delete them manually. then I decided to increase the vdwradii to 0.450 it is better now but i think the gap between water

[gmx-users] parallel running

Dear All I want to run gromacs in parallel on cluster.for this I follow below steps: 1-I connect to a node with ssh comand,fro example: ssh compute-o-1 2-cd scratch 3-grompp -f md.mdp-c input.gro-o output.tpr -p topol.top -n index.ndx 4- nohup mpirun -np 8 mdrun -de

Re: [gmx-users] parallel running

ource to your job. > Jianguo > ------ > *From:* mohsen ramezanpour > *To:* Discussion list for GROMACS users > *Sent:* Tuesday, 8 March 2011 17:26:19 > *Subject:* [gmx-users] parallel running > > Dear All > > I want to run gromacs in parallel

Re: [gmx-users] parallel running

On Tue, Mar 8, 2011 at 1:40 PM, Esztermann, Ansgar < ansgar.eszterm...@mpi-bpc.mpg.de> wrote: > > On Mar 8, 2011, at 10:26 , mohsen ramezanpour wrote: > > > 4- nohup mpirun -np 8 mdrun -deffnm output & > > > > The result is running mdrun on

Re: [gmx-users] parallel running

On Tue, Mar 8, 2011 at 2:53 PM, Esztermann, Ansgar < ansgar.eszterm...@mpi-bpc.mpg.de> wrote: > > On Mar 8, 2011, at 12:00 , mohsen ramezanpour wrote: > > > >> > Besides when I used the following command I get an executeable Error: > >> > mpirun

Re: [gmx-users] parallel running

On Tue, Mar 8, 2011 at 2:49 PM, Esztermann, Ansgar < ansgar.eszterm...@mpi-bpc.mpg.de> wrote: > > >> You don't use qsub or bsub? > > > > No,What is these?How can I prepare and use them? > > They are commands to submit jobs to batch systems. > > thank you.Please let me know more if it is possible T

Re: [gmx-users] parallel running

emkul wrote: > > > mohsen ramezanpour wrote: > > >> >> >> On Tue, Mar 8, 2011 at 2:49 PM, Esztermann, Ansgar < >> ansgar.eszterm...@mpi-bpc.mpg.de <mailto:ansgar.eszterm...@mpi-bpc.mpg.de>> >> wrote: >> >> >> >> You don

[gmx-users] Membrane Protein Tutorial

Dear All doing membrane protein tutorial of Dr.Justin I have a few question, Please let me know their answers. 1-Why do I need to use a tempreture upper than lipid phase transition tempreture for equilibration section? 2-What the lipid phase transition means exactly? Thanks in advance for you

[gmx-users] membrane-protein

Dear All doing membrane protein tutorial of Dr.Justin I have a few question, 1-Why do I need to know the stabilization state of my box vector? 2-How can I do this (with wich program?)? 3-What can I do if they were not stable? Thanks in advance Mohsen -- gmx-users mailing listgmx-users@gro

[gmx-users] membrane protein

Dear All in membrane protein tutorial: What is the P-N vector? RMSD for what group do I need to calculate? How can I estimate the helix tilt? Thanks in advance -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at

[gmx-users] versions

Dear All How can I read and work on outputs of one version of Gromacs with tools of other version? Because I have run my program on cluster(version 4.5.3) ,but I need to work with them in v.4.0.7 Suppose I have to work with this version and there is not any way to change versions neighter on clu

Re: [gmx-users] versions

t you to create a new topology > with the 4.0.7 version. > > > Il 12/03/2011 08:54, mohsen ramezanpour ha scritto: > > Dear All >> >> How can I read and work on outputs of one version of Gromacs with tools >> of other version? >> Because I have run my program o

Re: [gmx-users] versions

The exact Error is this: Program g_energy, VERSION 4.0.7 Source code file: ../../../../src/gmxlib/enxio.c, line: 118 Fatal error: You are trying to read an edr file of GROMACS version 4.1 or later with GROMACS version 4.0 On Sat, Mar 12, 2011 at 2:46 PM, mohsen ramezanpour < ramezanpour.

[gmx-users] terminated but not completely

Dear All I run a simulation for 4 days. Unfortunately it terminated,but not completely,1 steps from 2 has done. Is there any way to run the continue of my files? Thanks in advance for your guidances Best Regards -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/

[gmx-users] Grandcanonical Ensemble

Dear All 1-Does Gromacs support Grandcanonical ensemble too? 2-I want to increase the length of my simulation box during simulation,Is it possible? 3-As a result.I want to do my simulation in grandcanonical in the following way: As the length of my simulation box is increasing,I want to full the

[gmx-users] Umberella sampling

Dear All afew question in umberella sampling tutorial: 1-We do umberella sampling for each of 25 simulation windows,while using a spring(harmonic potential),Are these springs 1 or 3 dimensional? 2-Suppose the length of one windows is X nm,what is the approperiate K (spring constant) for this wind

[gmx-users] Pulling

Dear All Afew question about Pulling in Umberella Sampling 1-the goal of pulling is making some primary structures (in different distances) to do umberella sampling for each one of them. I can make these states by transporting my ligands along a vector to prepare these primary structures.Is this

Re: [gmx-users] Pulling

Dear Chris Thanks for your reply 2-When you limit your sampling phase space,it can make some Errors,Because you may ignore some important regions(where you don't know them and you can't predict there). In the other hands,When we pull drug along a line,although we had not restrain it, but in fact t

Re: [gmx-users] Umberella sampling

Dear chris Thanks for your reply 1-I am not sure,Since we need the know the variations of free energy along a specific degree of freedom of system(for example z axis),so the springs must be 1 dimensional to allow drug to oscilate only in one dimension(z axis). Let me say my question in other word

[gmx-users] Fwd: membrane protein

-- Forwarded message -- From: mohsen ramezanpour Date: Wed, Mar 9, 2011 at 2:49 PM Subject: membrane protein To: Discussion list for GROMACS users Dear All in membrane protein tutorial: What is the P-N vector? RMSD for what group do I need to calculate? How can I estimate

[gmx-users] Fwd: membrane-protein

-- Forwarded message -- From: mohsen ramezanpour Date: Tue, Mar 8, 2011 at 11:33 PM Subject: membrane-protein To: Discussion list for GROMACS users Dear All doing membrane protein tutorial of Dr.Justin I have a few question, 1-Why do I need to know the stabilization state of

Re: [gmx-users] Pulling

Thank you again for your reply On Wed, Mar 16, 2011 at 7:35 PM, wrote: > 2-When you limit your sampling phase space,it can make some Errors, >> Because you may ignore some important regions(where you don't know them >> and you can't predict there). >> > > I agree with the idea that underlies you

[gmx-users] g_rms & g-rmsd

Dear All I have a trajectory(.xtc) and its corresponding .tpr file: I used the following commands separately but the results were different,Why?? g_rms-f trajectory.xtc-s structure.tpr-n index.ndx-o rms.xvg I choosed group number 12 (drug in pulling problem) for two choose

[gmx-users] pick in pull.xvg

Dear All I did a pulling simulation for protein-drug system. My output (pull.xvg) has a pick in 100 ps (equivalent to 1 nm), the rest of plot is flat(of course with oscilation around the average),of course with NOT ZERO average in the flat region. Can I result ? " the interaction between protein

Re: [gmx-users] g_rms & g-rmsd

m once ;) > > Cheers, > > Tsjerk > > On Mar 19, 2011 12:16 PM, "mohsen ramezanpour" < > ramezanpour.moh...@gmail.com> wrote: > > Dear All > > > > I have a trajectory(.xtc) and its corresponding .tpr file: > I used the following commands s

[gmx-users] g_sham

Dear All I have a trajectory file for 500 ps simulation I used g_sham tool,the output was an ener.xvg file (0-40 on y axis and 0-33 on x axis ??!!) But I don't know what quantities are ploted via eachother? Please let me know Thanks in advance -- gmx-users mailing listgmx-users@gromacs.org h

[gmx-users] plot of force via time

Dear All I have a plot,Force via time.(pull.xvg in pulling) what is important,the value of force in each time or its average? because it is oscilationg around a line. I am in doubt , because the important in tempreture and pressure coupling were thier averages not their values in time. Thanks in

Re: [gmx-users] plot of force via time

> the list. > > Chris. > > -- original message -- > > plot of force via time > mohsen ramezanpour ramezanpour.mohsen at gmail.com > Sat Mar 19 14:49:40 CET 2011 > >* Previous message: [gmx-users] g_sham >* Messages sorted by: [ date ] [ thread ] [ subject

Re: [gmx-users] Is there still interest in rigid-body simulation?

Welcome :) It is absolutely useful. On Mon, Mar 28, 2011 at 2:32 AM, Adam Herbst wrote: > Hi all, > I have seen a few posts on gmx-users indicating a desire to treat certain > atom groups as rigid bodies in MD simulations. I just started implementing > this, and so far I have it working for tra

[gmx-users] domain decomposition

Dear All I have a file which contains afew residues (noncontinuous), When I use mdrun on a computer(4 cpu) I am facing with the following Error: Fatal error: There is no domain decomposition for 4 nodes that is compatible with the given box and a minimum cell size of 3.28697 nm Change the number

Re: [gmx-users] domain decomposition

raham wrote: > On 4/04/2011 1:51 AM, mohsen ramezanpour wrote: > >> Dear All >> >> I have a file which contains afew residues (noncontinuous), >> When I use mdrun on a computer(4 cpu) I am facing with the following >> Error: >> >> Fatal error: &g

Re: [gmx-users] domain decomposition

le of protein? Thanks in advance On Tue, Apr 5, 2011 at 11:58 AM, Mark Abraham wrote: > On 5/04/2011 5:09 PM, mohsen ramezanpour wrote: > >> Dear Mark >> >> Actually I don't know why. >> I just did the normal process as other my simulations. >> >> Let me

Re: [gmx-users] How to remove charge of 5e-2 ??

Dear Dr.Justin I had the same problem. I modified the charges and charge groupsin the topology of a drug.the net charge of it is zero(I am sure) though,when I used pdb2gmx it resulted a NOTE like the following: NOTE:The system has non-zero total charge: 3.03e00 I continued simulation and ign

Re: [gmx-users] How to remove charge of 5e-2 ??

Dear Dr.Justin What can we do (how can neutralize system) if the total charge of our system was not integer? I think there is not any solution and we have to simulate a charged system not a neutral. Am I right? Thanks in advance On Wed, Apr 6, 2011 at 11:12 AM, mohsen ramezanpour

Re: [gmx-users] How to remove charge of 5e-2 ??

Daer Dr.Mark You are right,But all of them(as I know) have integer charges! the problem is simullating a system with partial charges. We absolutely have such systems. On Wed, Apr 6, 2011 at 11:22 AM, Mark Abraham wrote: > On 6/04/2011 4:45 PM, mohsen ramezanpour wrote: > > Dear

Re: [gmx-users] How to remove charge of 5e-2 ??

Thank you. I read it and I understood your mean. On Wed, Apr 6, 2011 at 11:52 AM, Mark Abraham wrote: > On 06/04/11, *mohsen ramezanpour * wrote: > > Daer Dr.Mark > > You are right,But all of them(as I know) have integer charges! > the problem is simullating a system with par

Re: [gmx-users] How to remove charge of 5e-2 ??

rotein! I was wrong,we can't do that > Erik > > mohsen ramezanpour skrev 2011-04-06 09.13: > > Daer Dr.Mark > > You are right,But all of them(as I know) have integer charges! > the problem is simullating a system with partial charges. > We absolutely have such syst

[gmx-users] not enough space

Dear All I used mdrun for generating NVT It crashed and massage was: Trying to get md5sum: nvt-1.trr: Stale NFS file handle Trying to get md5sum: nvt-1.edr: Stale NFS file handle --- Program mdrun, VERSION 4.5.3-dev-20110310-a52f8-dirty Source

[gmx-users] Re: not enough space

(ns/day) (hour/ns) Performance:174.935 8.226 0.690 34.784 gcq#92: "Once Again Let Me Do This" (Urban Dance Squad) what it means? Why they worked if they were wrong?? On Wed, Apr 6, 2011 at 4:59 PM, mohsen ramezanpour < ramezanpour.moh...@gmail.com> wrote: >

[gmx-users] Umberella sampling

Dear Dr.Justin I had asked this question before but unfortunately I didn't answered good! Instead of Pulling and separating some structures in definite distances, I located my drug in definite distances along z axis (as my initial structures for doing umbrella sampling). Am I right? The main pro

Re: [gmx-users] Umberella sampling

Thank you very much Dr.Justin for your important notes On Wed, Apr 6, 2011 at 8:09 PM, Justin A. Lemkul wrote: > > > mohsen ramezanpour wrote: > >> Dear Dr.Justin >> I had asked this question before but unfortunately I didn't answered >> good! >>

[gmx-users] Extending Simulation

Dear All I used the following commands accoring to Extending Simulation in gromacs/Documentation/how-tos/Extending Simulation to extend my simulation. I entered: tpbconv -s npt-1.tpr-extend 100 -o npt-1-extend.tpr nohup mpirun -np 4 mdrun -s npt-1-extend.tpr -cpi npt-1.cpt Ii run this

[gmx-users] NPT.mdp parameters NOTE

Dear Dr.Justin As you have noticed in your tutorials,It is better to use Nose-Hoover for tempreture in the NPT.mdp file. You have used tau-t = 0.1 in most of your md.mdp files for generating npt ensemble. When I use a npt file with these settings,there is a Note as following: sorry,i can't rememb

Re: [gmx-users] Extending Simulation

Dear Dr.Mark On Sun, Apr 10, 2011 at 12:20 PM, Mark Abraham wrote: > On 10/04/2011 5:40 PM, mohsen ramezanpour wrote: > >> Dear All >> I used the following commands accoring to Extending Simulation in >> gromacs/Documentation/how-tos/Extending Simulation >> to exte

Re: [gmx-users] Extending Simulation

Dear Dr.Mark Thank you very much you are right I understood your mean exactly, On Sun, Apr 10, 2011 at 12:44 PM, Mark Abraham wrote: > On 10/04/2011 6:04 PM, mohsen ramezanpour wrote: > > Dear Dr.Mark > > On Sun, Apr 10, 2011 at 12:20 PM, Mark Abraham wrote: > >> On 10

[gmx-users] converging value

Dear All How can I determine the converged value of a simulation? Because the pressure has big oscilations around it's converging value but it is difficult to determine that value. can everybody guide me? Thanks in advance -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.o

Re: [gmx-users] converging value

file) Do you have any idea? I know it is not any problem if a quantity is oscilating around it's converged value. thanks in advance for your reply On Sun, Apr 10, 2011 at 3:09 PM, Mark Abraham wrote: > On 10/04/2011 6:48 PM, mohsen ramezanpour wrote: > >> Dear All >>

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

Hi peter I think the important is to don't couple small number of atoms(ligand molecules or a few ions) separately to a reference tempreture! It probably will result the same if you make two tcouple groups as below: Protein-LIG water-ions or Proteinwater-ions-LIG I think they will be equvale

[gmx-users] Articles using Gromacs to do simulation, calculation, evaluation

Dear All How can I get a list of all articles which have used Gromacs Package for their work? I looked at citations for 4 principal papers in gromacs website,but most of them were not simulations but improving algorithms such as lincs and etc. Some packages as Lammps saves articles which use lam

[gmx-users] Docking

Dear Users I read so many emails to mailing list, there were important notes about docking but I couldn't extract a general result. Please let me know: 1-Can we dock a ligand to it's protein's binding pocket with Pymol and Gromacs as following? first:locating ligand outside and close to binding

Re: [gmx-users] Docking

ote: > On 4/27/2011 7:05 PM, mohsen ramezanpour wrote: > >> Dear Users >> >> I read so many emails to mailing list, there were important notes about >> docking but I couldn't extract a general result. >> Please let me know: >> >> 1-Can we dock a

Re: [gmx-users] Docking

ham * escribió: > > > De: Mark Abraham > Asunto: Re: [gmx-users] Docking > A: "Discussion list for GROMACS users" > Fecha: miércoles, 27 de abril de 2011, 5:27 > > On 4/27/2011 7:52 PM, mohsen ramezanpour wrote: > > Dear Mark > Thank you for your reply.ye

[gmx-users] Continuation=yes From?

Dear Dr.Justin Regarding Umbrella Sampling tutorial: The CONTINUATION option in md_umbrella.mdp is YES, and you have noticed : From NPT I can't understand it's reason correctly! we run a NPT and then Pulling, then extracted some configurations from pull.trr file. I think we must continue from p

Re: [gmx-users] Continuation=yes From?

27 PM, Justin A. Lemkul wrote: > > > mohsen ramezanpour wrote: > >> Dear Dr.Justin >> >> Regarding Umbrella Sampling tutorial: >> >> The CONTINUATION option in md_umbrella.mdp is YES, >> and you have noticed : From NPT >> >> I can't u

Re: [gmx-users] Continuation=yes From?

Thank you for your detailed axplain I understood completely On Mon, May 2, 2011 at 4:34 PM, Justin A. Lemkul wrote: > > > mohsen ramezanpour wrote: > >> Dear Dr.Justin >> >> Thank you for your reply >> My is Protein-ligand,It is have the same conditions as

[gmx-users] Umberella sampling

Dear Dr.Justin Regarding doing umbrella sampling: I used gen_vel =no and I prefer to use from thermodynamics of system in NPT.cpt Although the T and P were as I did set in NPT.mdp file (T=310 ,P=1 bar) But their values in my umbrela.log files are not as before (for example P=-8.434578e+1) Wher

Re: [gmx-users] Umberella sampling

if I use NPT.enr OR NPT.trr OR in grompp(especially NPT.enr) ? Because all of information about NPT step are included in this files. Thanks in advance for your On Sun, May 8, 2011 at 5:47 PM, Justin A. Lemkul wrote: > > > mohsen ramezanpour wrote: > >> Dear Dr.Justi

Re: [gmx-users] Umberella sampling

t the information for npt ensemble. What do you think Thanks in advance for your reply On Sun, May 8, 2011 at 7:03 PM, Justin A. Lemkul wrote: > > > mohsen ramezanpour wrote: > >> Dear Dr.Justin >> >> I didn't any equilibration for any windows! Because: >>

Re: [gmx-users] Umberella sampling

Thank you very much I understood completely Best On Sun, May 8, 2011 at 7:30 PM, Justin A. Lemkul wrote: > > > mohsen ramezanpour wrote: > >> Dear Dr.Justin >> >> Thank you for your complete explanation. >> Please let me discribe where is NPT.cpt comes fro

Re: [gmx-users] how to obtain binding energy

Dear Shahab You need to do one of the following methods; 1-Umbrella Sampling and computing PMF curve 2-Thermodynamic Integration Please read some tutorials by Dr.Justin , It can be very useful Be success On Tue, May 17, 2011 at 3:08 PM, shahab shariati wrote: > Dear gromacs users > > > my sim

Re: [gmx-users] how to obtain binding energy?

Dear Shahab Yes,when you compute delta Gibbs energy of binding ,You can compute binding constant(Kd or Ki) by thermodynamics relations as Dr.Justin said. I think both methods can be applied to any systems which you wish to have its binding free energy. (including protein-protein,protein-ligand ,p

[gmx-users] PMF curve

Dear Dr.Justin Regarding to PMF curve which resulted from Umbrella sampling: I obtained the following curve. Dose it mean?Because it is not similar to yours in tutorial :( if yes,please let me know what is the Delta G value approximately? Because I don't know difference between which points is my

Re: [gmx-users] PMF curve

resultedin the whole of my curve. Is not it strong(wonderfull?)? On Mon, May 30, 2011 at 6:57 PM, Justin A. Lemkul wrote: > > > mohsen ramezanpour wrote: > >> Dear Dr.Justin >> >> Regarding to PMF curve which resulted from Umbrella sampling: >> I obtained the

Re: [gmx-users] PMF curve

, Justin A. Lemkul wrote: > > > mohsen ramezanpour wrote: > >> Thank you for your reply >> >> Actually my system is not the same as tutorial. >> > > Then you should not equate the results, or be concerned when things look > different. Every system is d

Re: [gmx-users] PMF curve

starting point? 0.18 (with negative value ) OR 0.03 (with about zero value) OR the average in that region? Because there is a difference about 0.5 kcal/mol . Thanks in advance On Mon, May 30, 2011 at 7:42 PM, Justin A. Lemkul wrote: > > > mohsen ramezanpour wrote: > >> Thank you

Re: [gmx-users] PMF curve

Dear Dr.Justin There is not any answer? On Mon, May 30, 2011 at 7:58 PM, mohsen ramezanpour < ramezanpour.moh...@gmail.com> wrote: > Yes,you are right > I need to do more sampling.But the second attached file was just to > transfer my mean :) > My final PMF curve is the f

Re: [gmx-users] PMF curve

On Mon, May 30, 2011 at 10:10 PM, Justin A. Lemkul wrote: > > > mohsen ramezanpour wrote: > >> Dear Dr.Justin >> >> There is not any answer? >> >> > Please have a bit of patience. I'm not your personal answer service. You > just happened t

[gmx-users] Gravity force in equation of motion

Dear All There is a question about applied forces in MD equations of motion. Where do we insert Gravity in our equation? In the other words : Had we ignored gravity force in our equations? Why? Actually I read manual but I weren't answered. Thanks in advance -- gmx-users mailing listgmx-use

Re: [gmx-users] Gravity force in equation of motion

Thank you for your reply. I think so On Wed, Jun 1, 2011 at 12:01 PM, Jianguo Li wrote: > Seems gravity is much weaker than the other forces in molecular simulations > and thus can be neglected. > Jianguo > > -- > *From:* mohsen ramezanpour >

[gmx-users] Published articles which have used Gromcas for their work

/About_Gromacs/Citations in the result of my search there are some articles which has not used gromacs but because of some reasons it has cited Gromacs. Please let me know how can I have a list of all publications by Gromacs. Thanks in advance for your guidances Best Mohsen Ramezanpour -- gmx-users

Re: [gmx-users] FEP

Hi Please have a look at Dr.Justin tutorial page at the following link: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/index.html Cheers On Mon, Oct 10, 2011 at 12:27 PM, Steven Neumann wrote: > Hi Gmx Users, > > Can you suggest some reading and some tutorial in calculat

Re: [gmx-users] pdb files from trajectory

Dear Shima What is the name of your .tpr file? If you had not chosen any name for it, Gromacs will generate a topol.tpr for you and in my idea this error will not occur, if not, you have to mention your file (e.g. Filename.tpr) explicitely in your command line! I hope this help you Best On Sun,

[gmx-users] umbrella Sampling and PMF- Error estimation

Hi everyone How can we have an error estimation for Gibbs binding free energy when I do umbrella sampling and PMF profile? Actually I did an umbrella sampling for protein and ligand complex and I have a PMF profile now but I do not know how much is my error! Thanks in advance for any suggestion

Re: [gmx-users] umbrella Sampling and PMF- Error estimation

Thank you for your reply Dr. Justin On 7/31/13, Justin Lemkul wrote: > > > On 7/31/13 7:00 AM, Mohsen Ramezanpour wrote: >> Hi everyone >> >> How can we have an error estimation for Gibbs binding free energy when >> I do umbrella sampling and PMF profile?

Fwd: [gmx-users] umbrella Sampling and PMF- Error estimation

ting of GBFE is 2 kj/mol ? Thanks in advance Best On 7/31/13, Mohsen Ramezanpour wrote: > Thank you for your reply Dr. Justin > > On 7/31/13, Justin Lemkul wrote: >> >> >> On 7/31/13 7:00 AM, Mohsen Ramezanpour wrote: >>> Hi everyone >>> >>>

[gmx-users] Entering ions

Dear users I want to use some ions in my simulation (Phosphorus, Sulfur and ...). How can I know in which FF these are present? And what can I do if no FF include the interested Ions? any suggestion is appreciated in advacne Best Mohsen -- gmx-users mailing listgmx-users@gromacs.org http://

Re: [gmx-users] Entering ions

Dear Dr. Justin Thank you for your reply You are right, I am sorry for my mistake. I meant Phosphate and Sulfate ions. I want to have these ions in my solution. On Mon, Oct 21, 2013 at 1:37 PM, Justin Lemkul wrote: > > > On 10/21/13 4:45 AM, Mohsen Ramezanpour wrote: > &

Re: [gmx-users] Entering ions

sure, thank you. On Mon, Oct 21, 2013 at 4:49 PM, Justin Lemkul wrote: > > > On 10/21/13 8:54 AM, Mohsen Ramezanpour wrote: > >> Dear Dr. Justin >> >> Thank you for your reply >> >> You are right, I am sorry for my mistake. I meant Phosphate and Sulfat

[gmx-users] Please guide me

Dear All I am running a seamulated anneaking + MD in my cluster. I had done it for 2 times. but my results are not as i expect. I have attached my md.mdp file for you,I don't know which part of it is wrong. what i like to result is to change tempreture from 420 in 0 ps to 450 in 20 ps and then gra

Re: [gmx-users] Please guide me

I am not sure. How can I check it? I think as you.but I don't know what and how can I modify it. On Thu, Oct 14, 2010 at 1:52 PM, ms wrote: > On 14/10/10 08:51, mohsen ramezanpour wrote: > >> Dear All >> >> I am running a seamulated anneaking + MD in my cluster.

Re: [gmx-users] Please guide me

ocourse my running took a few hours time.is it possible crashing? On Thu, Oct 14, 2010 at 2:54 PM, mohsen ramezanpour < ramezanpour.moh...@gmail.com> wrote: > I am not sure. > How can I check it? > I think as you.but I don't know what and how can I modify it. > > >

[gmx-users] PRODRG server

Dear gromacs users I have a pdb file who include protein and a drug.I separated them by pymol software and saved them separately.now I want to make topology and gro file for it but I am facing with this page below.can you guid me? thanks in advance. PRODRG> Starting up PRODRG version 071121.0636

Re: [gmx-users] simulation of a protein including calcium ion

0 at 11:32 AM, mohsen ramezanpour < ramezanpour.moh...@gmail.com> wrote: > Hi > I think it is a typical ligand in your pdb file.what do you think? > if it be a ligand you can use PRODRG server to make topology file for your > ligand and you must edit other files. > please re

[gmx-users] Re: PRODRG server

actually the final massage was :Unfortunately PRODRG crashed On Sat, Oct 16, 2010 at 11:36 AM, mohsen ramezanpour < ramezanpour.moh...@gmail.com> wrote: > Dear gromacs users > > I have a pdb file who include protein and a drug.I separated them by pymol > software and saved the

Re: [gmx-users] simulation of a protein including calcium ion

On Sat, Oct 16, 2010 at 12:00 PM, leila karami wrote: > Dear mohsen ramezanpour* * > > yes. calcium is a typical ligand in my pdb file.I used PRODRG server to make > topology file but > > ERRDRG> Too many atoms in this molecule (should be <=300). > PRODRG> Pro

Re: [gmx-users] simulation of a protein including calcium ion

Dear Leila Yes,I think so please read the article who I pointed,It can help you On Sat, Oct 16, 2010 at 12:16 PM, leila karami wrote: > Dear mohsen ramezanpour > > > my pdb file has 3000atoms (protein) + 1 atom (calcium). > > Should I separate ion from general pdb again?

Re: [gmx-users] Re: PRODRG server

RODRG> WARNING: bond type assignment failed at C13 > > There is something about the chemical structure involving this atom that > PRODRG can't handle. Based on the information you've provided, however, > there's no real way anyone can give you much advice. Have you tried dra

[gmx-users] analysis

Dear Gromacs users I am searching for a good text for underestanding analysis tools. Of course I had read the user manual (chapter 8),But I think I need more about them.for example I want a mathematical description and an easy explanation of analysis tool's results from a MD trajectory. Please let

Re: [gmx-users] analysis

Dear justin Thank you I will do that. On Sun, Oct 17, 2010 at 7:12 PM, Justin A. Lemkul wrote: > > > mohsen ramezanpour wrote: > >> Dear Gromacs users >> >> I am searching for a good text for underestanding analysis tools. >> Of course I had read the user m

Re: [gmx-users] Gibbs free energy of binding

Dear Gromacs users I want to calculate Gibbs free energy too,but about Protein-drug binding. Please guide more clearly,what texts I need to read for learning how can I do it? Besides,g-energy has an option for estimating free energy from trajectory file(-fee option) I thought if I had a trajectory

Re: [gmx-users] Gibbs free energy of binding

g_sham? On Wed, Oct 20, 2010 at 2:28 PM, Justin A. Lemkul wrote: > > > mohsen ramezanpour wrote: > >> Dear Gromacs users >> >> I want to calculate Gibbs free energy too,but about Protein-drug binding. >> Please guide more clearly,what texts I need to

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