Re: [gmx-users] make_edi, g_covar -nofit

On May 4, 2010, at 10:56 PM, vijaya subramanian wrote: > Hi Carsten > A couple of quick questions: > I already have gromacs-4.0.7 downloaded from the gromacs website. I found > that I couldn't > use git checkout --track -b release-4-0-patches origin/release-4-0-patches to > get the patches. >

Re: [gmx-users] PMF profile using g_wham with pull_geometry = distance for ion channel

Thomas Piggot wrote: Hi, I am trying to construct a PMF profile for a phosphate ion passing through a membrane protein using umbrella sampling with GROMACS 4.0.5. I have performed the umbrella sampling simulations using the following mdp options and I am now attempting to construct the PMF u

Re: [gmx-users] PMF profile using g_wham with pull_geometry = distance for ion channel

Jochen thanks for your help. That was what I was afraid of you saying. Oh well, at least this will hopefully provide a useful reference so somebody doesn't make this same mistake. On a side note I noticed a couple of small issues with g_wham. Firstly the -wcorr option says Input, opt. not Ou

Re: [gmx-users] PMF profile using g_wham with pull_geometry = distance for ion channel

Thomas Piggot wrote: Jochen thanks for your help. That was what I was afraid of you saying. Oh well, at least this will hopefully provide a useful reference so somebody doesn't make this same mistake. On a side note I noticed a couple of small issues with g_wham. Firstly the -wcorr option s

Re: [gmx-users] PMF profile using g_wham with pull_geometry = distance for ion channel

Hi again, Just before I reside myself to rerunning a large number of simulations I was wondering if it is possible to just rerun the simulations where the ion is above and below the reference using pull_geometry=position. Then could I combine these with the other simulations where pull_geomet

RE: [gmx-users] electro-static potential energy after minimization

Thank you for your replies. You guys were right about the problem. The effect of the electrostatic interaction was being masked by the contribution of water to the coulombic energy. I wanted to ask if there was some way to run minimization or MD in a vacuum? I only started using GROMACS last

Re: [gmx-users] Hydrogen Bond Residence Time

Anirban Ghosh skrev: Hi ALL, How can I obtain the residence time of each hydrogen bond during a simulation? I think the -hbn and -hbm options of g_hbond has to be used, but how? Is there any script to extract that data? And what is the difference between the residence time and the life time o

Re: [gmx-users] electro-static potential energy after minimization

On 5/05/2010 11:44 PM, abdullah ahmed wrote: Thank you for your replies. You guys were right about the problem. The effect of the electrostatic interaction was being masked by the contribution of water to the coulombic energy. *I wanted to ask if there was some way to run minimization or MD in a

[gmx-users] Re: PMF profile using g_wham with pull_geometry = distance for ion channel

Dear Tom: Your idea will work, but only for the one replica centered exactly at 0.0; the other ones will need to be rerun. But you really should not need to rerun very many replicas, unless I misunderstand your setup. The problem is this: if your center of restraint is close enough to 0.0

RE: [gmx-users] make_edi, g_covar -nofit

Hi No, the original gromacs-4.0.7 installation was not a clone from the repository. So I uninstall that, and install the clone after getting the patches? Thanks Vijaya From: ckut...@gwdg.de Subject: Re: [gmx-users] make_edi, g_covar -nofit Date: Wed, 5 May 2010 09:49:22 +0200 To: gmx-users@gr

Re: [gmx-users] make_edi, g_covar -nofit

Hi, On May 5, 2010, at 5:01 PM, vijaya subramanian wrote: > Hi > No, the original gromacs-4.0.7 installation was not a clone from the > repository. > So I uninstall that, and install the clone after getting the patches? This would be convenient since for more bug fixes you would then just need

[gmx-users] question about installing gromacs on a mac

I apologize in advance if this is a very stupid question. I am trying to configure GROMACS on a mac. I have the intel MKL installed. *When I type the following:* ./configure --with-fft=mkl CPPFLAGS="-I/Developer/opt/intel/Compiler/11.1/067/Frameworks/mkl/include" LDFLAGS="-L/Developer/opt/intel

[gmx-users] issue with nsteps

Dear all I am having a problem with a Gromacs run that I have prepared for a total of 1e10 steps (actually nsteps=100; this accounts in this case for a total run time of 10 microseconds). When I run "grompp" I see in the preprocessing output that apparently the correct number of steps h

Re: [gmx-users] question about installing gromacs on a mac

Hi, I have never tried to compile gromacs with MKL, but you could try to configure with CFLAGS="-framework mkl" Hope this helps, Rui Rodrigues On Wed, 5 May 2010 12:15:23 -0400, Emily Curtis wrote > I apologize in advance if this is a very stupid question. I am trying to > configure GROMACS

Re: [gmx-users] issue with nsteps

On 5/5/10 6:42 PM, DAVID DE SANCHO wrote: Dear all I am having a problem with a Gromacs run that I have prepared for a total of 1e10 steps (actually nsteps=100; this accounts in this case for a total run time of 10 microseconds). When I run "grompp" I see in the preprocessing output th

[gmx-users] Mac OS X with MKL

Hi. I am also trying to build Gromacs with MKL on a Mac OS X. I get the same error that you reported: checking for mkl.h... yes checking for DftiComputeForward in -lmkl... no configure: error: Cannot find Intel Math Kernel Library >= 6.0 Did you ever figure out how to fix this? I would reall

Re: [gmx-users] Mac OS X with MKL

Emily Curtis wrote: Hi. I am also trying to build Gromacs with MKL on a Mac OS X. I get the same error that you reported: checking for mkl.h... yes checking for DftiComputeForward in -lmkl... no configure: error: Cannot find Intel Math Kernel Library >= 6.0 Did you ever figure out how to

Re: [gmx-users] Mac OS X with MKL

On 6/05/2010 6:15 AM, Justin A. Lemkul wrote: Emily Curtis wrote: Hi. I am also trying to build Gromacs with MKL on a Mac OS X. I get the same error that you reported: checking for mkl.h... yes checking for DftiComputeForward in -lmkl... no configure: error: Cannot find Intel Math Kernel Libr

Re: [gmx-users] how to show structure results in Martini coarse-grained simulation?

Dear Sir : The script require what format for top file? my top file is here: ; ; Example topology file for MARTINI 2.0 ; ; First include the file containing all particle definitions, ; the interaction matrix, plus the topology for water. #include "martini_v2.1.itp" #include "martini_v2.0_ions.it

Re: [gmx-users] how to show structure results in Martini coarse-grained simulation?

xi zhao wrote: Dear Sir : The script require what format for top file? my top file is here: The input is the actual protein topology, not the system topology. -Justin ; ; Example topology file for MARTINI 2.0 ; ; First include the file containing all particle definitions, ; the interacti

Re: [gmx-users] Mac OS X with MKL

Sorry for my bad english... That happens to me but in linux. If you are using mkl >= 10 you need to change the way the libraries are called. Search the configuration file for the lines were the mkl are called. Search for -lmkl and change -lmkl with -lmkl_i n t e l_lp64 -lmkl_sequential -lmkl_core

Re: [gmx-users] Mac OS X with MKL

Anthony, Thank you very much Your suggestions worked! I really appreciate your help...I have been trying to figure this out for hours! Have a good night! Emily On Wed, May 5, 2010 at 9:55 PM, Anthony Cruz Balberdi wrote: > Sorry for my bad english... That happens to me but in linux. If y

Re: [gmx-users] how to show structure results in Martini coarse-grained simulation?

in fact, how to deal with format problem in coarse-grained ? thank you! --- 10年5月6日，周四, Justin A. Lemkul 写道： 发件人: Justin A. Lemkul 主题: Re: [gmx-users] how to show structure results in Martini coarse-grained simulation? 收件人: "Gromacs Users' List" 日期: 2010年5月6日,周四,上午9:40 xi zhao wrote:

Re: [gmx-users] how to show structure results in Martini coarse-grained simulation?

xi zhao wrote: in fact, how to deal with format problem in coarse-grained ? What do you mean? -Justin thank you! 4 --- *10年5月6日，周四, Justin A. Lemkul //* 写道：

Re: [gmx-users] how to show structure results in Martini coarse-grained simulation?

produce input file , in coarse grained , no standard protein top file --- 10年5月6日，周四, Justin A. Lemkul 写道： 发件人: Justin A. Lemkul 主题: Re: [gmx-users] how to show structure results in Martini coarse-grained simulation? 收件人: "Gromacs Users' List" 日期: 2010年5月6日,周四,上午10:37 xi zhao wrote:

Re: [gmx-users] how to show structure results in Martini coarse-grained simulation?

xi zhao wrote: produce input file , in coarse grained , no standard protein top file I still don't understand what your question is. Are you still having problems with top2psf? If so, please explain what the difficulty is or what exactly you're trying to do. -Justin 4

[gmx-users] Lipid topologies, carving, etc

Hi everyone, I am setting up an ion channel in a lipid, and in the past I would manually carve the membrane using something like PyMol. This time tried the very nice automatic system builder at http://www.charmm-gui.org/?doc=input/membrane and the result is beautiful. However, the POPC isn't comp

Re: [gmx-users] Lipid topologies, carving, etc

On 6/05/2010 1:58 PM, Alex Smolyanitsky wrote: Hi everyone, I am setting up an ion channel in a lipid, and in the past I would manually carve the membrane using something like PyMol. This time tried the very nice automatic system builder at http://www.charmm-gui.org/?doc=input/membrane and the

[gmx-users] PMF of ligand transport

Hi gromacs users, I am using Gromacs 4.0.4 package. I am doing SMD of a ligand transport through a channel. I performed SMD and did umbrella sampling (Thanks to Justin for his tutorial). Extracted frames with a window spacing interval of ~0.12nm. and did 1ns sampling. Histograms are with reasona