[gmx-users] (no subject)

Subject: Ion jump out of protein after MD Date: Sat, 14 Mar 2009 09:45:28 +0330 Message-Id: <20090314061153.m77...@razi.tums.ac.ir> X-Mailer: OpenWebMail 2.53 20081220 334 X-OriginatingIP: 194.225.58.210 (hazizian) MIME-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Hi Sorry I r

[gmx-users] about MARTINI forcefield

Hi MARTINI forcefield users, I am very interesting in using the MARTINI forcefield for simulating my molecules, But I am not very familiar with it. So I hope some kind people can help me about its application. I want to know if It is suitable for the molecules of attached figures. It have TWO

[gmx-users] problem with pull direction

Hello gmx-users, I find the pulling direction in PULL INFO section of the log file is not coincident with the afm_dir1 parameter i defined in the pull.ppa. could some one tell me which direction is actually used in the pulling process? Thank you very much. Huifang Liu -- Huifang Liu (Ph.D.

Re: [gmx-users] Matching atom name and types in OPLS-aa FF

Tree wrote: Dear All: I appreciate your answer always. Right now, I am trying to add/modify some values in OPLS-aa FF. I am confused atom type (opls_xxx) and atom name (e.g., C) in "atp", "bon.itp", and "nb.itp" files. Please let me try the situation by an example, first. In "atp" file,

[gmx-users] Fwd: Matching atom name and types in OPLS-aa FF

Since I cannot see my message on the gmx-users mail list, I am forwarding this again.I am sorry to bother your email box again... Hope you would understand... -- Forwarded message -- From: Tree Date: Fri, Mar 13, 2009 at 8:51 PM Subject: Matching atom name and types in OPLS-aa FF

[gmx-users] Matching atom name and types in OPLS-aa FF

Dear All: I appreciate your answer always. Right now, I am trying to add/modify some values in OPLS-aa FF. I am confused atom type (opls_xxx) and atom name (e.g., C) in "atp", "bon.itp", and "nb.itp" files. Please let me try the situation by an example, first. In "atp" file, ... opls_058

Re: [gmx-users] gtkmm Code Demos?

Thank you for your response to my most recet post. I did compile without the --enable-shared and got the same result. Mark Abraham wrote: Stephen P. Molnar wrote: The demo to which I was referring is /sdb5/Applications/gromacs/share/gromacs/tutor/gmxdemo (sorry about that, it was a direct re

Re: [gmx-users] Triclinic water box for a protein MD

This looks great thanks, had meant to try and implement something like these restraints for ages but never got round to it, you know how it is ... Tom --On 13 March 2009 21:06 +0100 Tsjerk Wassenaar wrote: Or, you use our server (http://haddock.chem.uu.nl/Squeeze/) to get an optimally packed

Re: [gmx-users] Triclinic water box for a protein MD

Or, you use our server (http://haddock.chem.uu.nl/Squeeze/) to get an optimally packed system and simulate it with the Gromacs 3.3.1 version you can download from http://nmr.chem.uu.nl/~tsjerk/GMX/gromacs-3.3.1-rtc.tgz That version of gromacs has the roto-translational constraints implemented that

Re: [gmx-users] gtkmm Code Demos?

Stephen P. Molnar wrote: The demo to which I was referring is /sdb5/Applications/gromacs/share/gromacs/tutor/gmxdemo (sorry about that, it was a direct result of my memory) The configure command line that I used was "configure --prefix=/sdb5/Applications/gromacs --exec-prefix=/sdb5/Applicati

Re: [gmx-users] problem in energy minimization

Abhik Mukhopadhyay wrote: Hi Jastin My pdb2gmx command line is pdb2gmx -ignh -f xx.pdb -o xxout.pdb -p xx.top -water spce When I created the topology it did not create a bond between those two residues (between which the part is missing). The above statement seems inconsistent with the observ

Re: [gmx-users] Energy/temperature drifts in Gromacs 4.0 / inconsistencies with Gromacs 3.3.1

ADDENDUM: I've just compiled Gromacs 3.3.3 on cluster NEW, with Intel compiler (see below). A simulation (still running) on system 2 with the paralled double-prec version shows preliminary results in line with gromacs 3.3.1 on cluster OLD, with no trace of abnormal oscillations and drifts in temper

Re: [gmx-users] Triclinic water box for a protein MD

You might want to try a rombic dodecahedron box (an option in editconf). Or you can run the simulation using a triclinic box hoping the images don't interact and then check after the simulation has finished using g_mindist -pi on the trajectory, bearing in mind if they do then you will have was

Re: [gmx-users] Triclinic water box for a protein MD

Hi, You have to make sure that you're molecule doesn't rotate. Otherwise it will cause direct interactions over the PBC. The same holds true for large conformational changes. Cheers, Tsjerk On Fri, Mar 13, 2009 at 7:26 PM, Justin A. Lemkul wrote: > > > Lucio Montero wrote: >> >> I want to simu

Re: [gmx-users] Energy/temperature drifts in Gromacs 4.0 / inconsistencies with Gromacs 3.3.1

> That was a long mail. How about T-coupling? Which algorithm did you use? Sorry for the long mail. For T-coupling I used Berendsen al gorithm. > Did you do a diff on the md.log to check for differences in the mdp > parameters? Yes, I attach the diff file (emended of references and other comment

Re: [gmx-users] Triclinic water box for a protein MD

Lucio Montero wrote: I want to simulate a protein complex using a triclinic box, because it reduce my system size in 60%, and consequently the computing time. I have read that using a triclinic box can give problems for a long MD if the peptide has a whirl, but I don´t know if it is a problem

Re: [gmx-users] using more than one type of molecules

Molecular Dynamics wrote: Dear All, I'm new to Gromacs and have some questions to learn the answers. I study on one type molecule. If I want to add lets say 240 molecules, which is the best way to use editconf or genbox ? And I learned the procedure of using more than one type of molecul

[gmx-users] using more than one type of molecules

Dear All, I'm new to Gromacs and have some questions to learn the answers. I study on one type molecule. If I want to add lets say 240 molecules, which is the best way to use editconf or genbox ? And I learned the procedure of using more t

[gmx-users] Triclinic water box for a protein MD

I want to simulate a protein complex using a triclinic box, because it reduce my system size in 60%, and consequently the computing time. I have read that using a triclinic box can give problems for a long MD if the peptide has a whirl, but I don´t know if it is a problem for a complex of ~ 530

Re: [gmx-users] gtkmm Code Demos?

The demo to which I was referring is /sdb5/Applications/gromacs/share/gromacs/tutor/gmxdemo (sorry about that, it was a direct result of my memory) The configure command line that I used was "configure --prefix=/sdb5/Applications/gromacs --exec-prefix=/sdb5/Applications/gromacs --enable-share

Re: [gmx-users] Energy/temperature drifts in Gromacs 4.0 / inconsistencies with Gromacs 3.3.1

Pietro Amodeo wrote: Hi Gromacs users/developers, we have two Gromacs installations on two different clusters with the following sw versions: 1) Cluster: OLD(Myrinet) Gromacs 3.3.1 (CentOS 4 / Rocks 4.1) kernel 2.6.9-22.ELsmp gcc 3.4.4 fftw 3.1.2 mpich-gm 1.2.7p1..18 2) Clust

Re: [gmx-users] problem in energy minimization

Hi Jastin My pdb2gmx command line is pdb2gmx -ignh -f xx.pdb -o xxout.pdb -p xx.top -water spce When I created the topology it did not create a bond between those two residues (between which the part is missing). Thanks for your suggestion. Abhik Abhik Mukhopadhyay Departamento Química / Fac

[gmx-users] Energy/temperature drifts in Gromacs 4.0 / inconsistencies with Gromacs 3.3.1

Hi Gromacs users/developers, we have two Gromacs installations on two different clusters with the following sw versions: 1) Cluster: OLD(Myrinet) Gromacs 3.3.1 (CentOS 4 / Rocks 4.1) kernel 2.6.9-22.ELsmp gcc 3.4.4 fftw 3.1.2 mpich-gm 1.2.7p1..18 2) Cluster: NEW(Infiniband)

Re: [gmx-users] Variance in ED

Hi Andrea, You're welcome. I forgot to mention that my MD tutorial also has a part dedicated to PCA: http://nmr.chem.uu.nl/~tsjerk/course/molmod/analysis.html Maybe you'll find it useful. Cheers, Tsjerk On Fri, Mar 13, 2009 at 4:44 PM, andrea carotti wrote: > Dear Dr. Wassenaar, > many thank

[gmx-users] Variance in ED

Dear Dr. Wassenaar, many thanks for your kind reply. Andrea -- Andrea Carotti Dipartimento di Chimica e Tecnologia del Farmaco Università di Perugia Via del Liceo, 1 06123 Perugia, Italy phone: +39 075 585 5169 fax: +39 075 585 5161 www http://rpg.unipg.it personal www h

Re: [gmx-users] make hole with gromacs 3.1.4 error : Unknown left-hand iconstraint_algorithm in parameter file

sitiazma wrote: Hi gromacs users, does anyone knows why I got this error from grompp > grompp -f run.mdp -o dmpc.tpr -c dmpc.pdb -n index.ndx -p topol.top WARNING 1 [file run.mdp, line unknown]: Unknown left-hand iconstraint_algorithm in parameter file Yep. Like the message says, it's bec

Re: [gmx-users] get a box of 100 molecules

Adrien Delmont wrote: What are the suitable options for Chirality , Full charges , Energy Minimization in PRODRG to get input files for hydrocarbon molecules ? And If I choose Full charges : YES , I will get the files that include charge info. Can I erase the charge info and write the c

Re: [gmx-users] make hole with gromacs 3.1.4 error : Unknown left-hand iconstraint_algorithm in parameter file

sitiazma wrote: Hi gromacs users, does anyone knows why I got this error from grompp > grompp -f run.mdp -o dmpc.tpr -c dmpc.pdb -n index.ndx -p topol.top WARNING 1 [file run.mdp, line unknown]: Unknown left-hand iconstraint_algorithm in parameter file You have a typo. The error messa

[gmx-users] make hole with gromacs 3.1.4 error : Unknown left-hand iconstraint_algorithm in parameter file

Hi gromacs users, does anyone knows why I got this error from grompp > grompp -f run.mdp -o dmpc.tpr -c dmpc.pdb -n index.ndx -p topol.top WARNING 1 [file run.mdp, line unknown]: Unknown left-hand iconstraint_algorithm in parameter file I run gromacs 3.1.4 to make a hole in lipids using MSMS

Re: [gmx-users] get a box of 100 molecules

What are the suitable options for Chirality , Full charges , Energy Minimization in PRODRG to get input files for hydrocarbon molecules ? And If I choose Full charges : YES , I will get the files that include charge info. Can I erase the charge info and write the charge info I got from Gaussi

Re: [gmx-users] get a top file to run md simulation

oguz gurbulak wrote: Dear Users, I'm trying to obtain .gro and top files successfuly for my n-alkanes molecules and want to run md simulations both using oplsaa and Gromos96 force fields seperately. Then I will compare the results of two md runs. I think that I can generate itp files for Gr

[gmx-users] get a top file to run md simulation

Dear Users, I'm trying to obtain .gro and top files successfuly for my n-alkanes molecules and want to run md simulations both using oplsaa and Gromos96 force fields seperately. Then I will compare the results of two md runs. I think that I can generate itp files for Gromos96 force fields  using p

Re: [gmx-users] gtkmm Code Demos?

Stephen P. Molnar wrote: Due to an unfortunate loss of my working copy I have had to recompile gromacs-4.0.4 on my OpenSuSE 10.3 computer. I encountered no problems but when I attempt to run demo I get a popup box labeled gtkmm Code Demos. This is accompanied by an error message "** (demo:1

[gmx-users] Re: Fwd: Ligand is moving far away after energy minimization

Please keep all Gromacs-related messages on the gmx-users list. Ms. Aswathy S wrote: Dept. Biotechnology Ext. 3108 - Forwarded Message - From: "Ms. Aswathy S" To: "gmx-users" Sent: Thursday, March 12, 2009 8:19:42 PM GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi Subject: Ligand is

RE: [gmx-users] free energy coupling/decoupling equivalence

Hi, If you are talking about equilibrium methods, for instance free energy intergration or Bennett's acceptance ratio, there is no directionality. You might start a simulations at a lamba point with the end configuration of the previous lambda, which could introduce some directionality, but the

[gmx-users] wall modelling

Dear ALL, I wish to model a wall which is tethered to its position by a harmonic spring. In a wall model all the atoms are monoatomic and hence they do not bond with the other wall atom. How then to define a potential which will fix each atom to its position in form of a harmonic bond. -- Avinas

RE: [gmx-users] viscosity calculation using g_energy (3.3.3)

Hi, I don't understand what you are actually doing now. You seem to be mixing multiple methods. First off all, I would use NPT for all methods, except the one that uses the pressure fluctuation. The pressure will have a large effect on the viscosity and if you run NVT you need to have exactly

[gmx-users] gtkmm Code Demos?

Due to an unfortunate loss of my working copy I have had to recompile gromacs-4.0.4 on my OpenSuSE 10.3 computer. I encountered no problems but when I attempt to run demo I get a popup box labeled gtkmm Code Demos. This is accompanied by an error message "** (demo:19437): WARNING **: Cannot

Re: [gmx-users] problems with gmxtest.pl

Dear users and developers, the tests were run on one node of a linux cluster employing 8 cores. Each node is a dual socket blade with two quad core cpus. /proc/cpuinfo says: processor : 0 vendor_id : GenuineIntel cpu family : 6 model : 23 model name : Intel(R) Xeon

Re: [gmx-users] problems with gmxtest.pl

bandow wrote: Dear users and developers of gromacs, despite checking for the usage of the proper version of tests after upgrading to gromacs-4.0.4 the test suite still produces results with the status FAILED. This is the case for some tests in kernel, complex, and pdb2gmx. For example kernel020

Re: [gmx-users] Fwd: Force Field - Gromos96

Hi C Kim, The GROMOS96 force _is_ a united atom force field. Cheers, Tsjerk On Fri, Mar 13, 2009 at 5:30 AM, Tree wrote: > > > -- Forwarded message -- > From: tree > Date: Thu, Mar 12, 2009 at 10:09 PM > Subject: Force Field - Gromos96 > To: gmx-users@gromacs.org > > > Dear Al

Re: [gmx-users] Force Field - Gromos96

On Mar 13, 2009, at 3:09 AM, tree wrote: Dear All: I appreciate it if it would be possible for me to have an answer related to Gromos96 force field. I am hoping to know if the Gromos96 force field can support All-Atom calculation? (Or does it 'only' support Unified Atom simulation?) O

Re: Re: [gmx-users] viscosity calculation using g_energy (3.3.3)

 Dear Berk and David, Thank you very much for your appropriate and informative replies. I tried another method (traverse current method) to calculate the shear viscosity ( a non equilibrium method, which has been described in Berkś paper : Journal of C

[gmx-users] Re: Hardware suggestion

Sedat Çapar wrote: Hello, We are a project group and we are planning to work with gromacs. Firstly, we will purchase a computer to run gromacs. I am planning to purchase a SUN server or workstation since I think they may outperform any PC but I'm not sure. I investigated your web site but I coul