Re: [gmx-users] how to calculate the conc in the genion

On Fri, Aug 12, 2011 at 8:08 AM, Mark Abraham wrote: > On 12/08/2011 2:22 AM, lina wrote: >> >> On Thu, Aug 11, 2011 at 11:35 PM, Tsjerk Wassenaar >>  wrote: >>> >>> Hi, >>> > I'd be amazed if the error was in the code and not in your calculation. > The > number of water molecules does

[gmx-users] Trouble installing mdrun-gpu from gromacs 4.5.4 package

Hi, I've checked for both libraries, they both are installed (CUDA is most definitely installed as it is used for other applications on the computer I am trying to build the mdrun-gpu binary on).-Smitty -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/g

Re: [gmx-users] compile template.c

On 12/08/2011 7:48 AM, Park, Jae Hyun nmn wrote: Dear GMX users, Now, I am trying to write my own gromacs analysis code with gromacs 4.5.3. As a first test, when I run "make" in the directory of "template" I got the following message: -- cc -O3 -fomit-frame-pointer

Re: [gmx-users] how to calculate the conc in the genion

On 12/08/2011 2:22 AM, lina wrote: On Thu, Aug 11, 2011 at 11:35 PM, Tsjerk Wassenaar wrote: Hi, I'd be amazed if the error was in the code and not in your calculation. The number of water molecules doesn't matter for the calculation of the ion concentration, of course. Pay attention to your

Re: [gmx-users] Topology for a new ligand

On 12/08/2011 1:48 AM, Kavyashree M wrote: Dear users, I was mentioning about OPLSAA force field for ATP and other small molecule. I just wanted to know the procedure to be followed and some guidance from people who have created topologies for such molecules manually. I am going through chapter

[gmx-users] compile template.c

Dear GMX users, Now, I am trying to write my own gromacs analysis code with gromacs 4.5.3. As a first test, when I run "make" in the directory of "template" I got the following message: -- cc -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -msse2 -fun

[gmx-users] compile template.c

Dear GMX users, Now, I am trying to write my own gromacs analysis code with gromacs 4.5.3. As a first test, when I run "make" in the directory of "template" I got the following message: -- cc -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -msse2 -fun

Re: [gmx-users] how to calculate the conc in the genion

Hey Justin, > I'm wondering if you can elaborate a bit on this.  I can understand your > point in the case of interfacial systems, membranes, or other biphasic > systems, but for a protein in water, why does the volume occupied by the > protein matter?  All components - protein, water, ions - are

Re: [gmx-users] Topology for a new ligand

Kavyashree M wrote: Dear users, I was mentioning about OPLSAA force field for ATP and other small molecule. I just wanted to know the procedure to be followed and some guidance from people who have created topologies for such molecules manually. I am going through chapter 5 of the manual. But

Re: [gmx-users] reg genion

vidhya sankar wrote: Dear justin, Thank you for your previous mail I am using genion pro gramme if i use genion programme using random option in number of times Then will it add positive and negative ions in different (xyz) coordinate in every time ot

Re: [gmx-users] Regarding parametrisation

Ravi Kumar Venkatraman wrote: Dear Justin, I was reading one of your literature on building GROMOS-compatible small molecule topologies. I was trying to reproduce the AM1BCC partial charges for the p-cresol using Antechamber from amber tools version 1.5. This is a newer

Re: [gmx-users] how to calculate the conc in the genion

Tsjerk Wassenaar wrote: Hi, I'd be amazed if the error was in the code and not in your calculation. The number of water molecules doesn't matter for the calculation of the ion concentration, of course. Pay attention to your box shape. And do consider the number of ions has to be an integer, s

Re: [gmx-users] how to calculate the conc in the genion

On Thu, Aug 11, 2011 at 11:35 PM, Tsjerk Wassenaar wrote: > Hi, > >>> I'd be amazed if the error was in the code and not in your calculation. The >>> number of water molecules doesn't matter for the calculation of the ion >>> concentration, of course. Pay attention to your box shape. And do consid

Re: [gmx-users] Topology for a new ligand

Dear users, I was mentioning about OPLSAA force field for ATP and other small molecule. I just wanted to know the procedure to be followed and some guidance from people who have created topologies for such molecules manually. I am going through chapter 5 of the manual. But wanted some useful sugg

Re: [gmx-users] how to calculate the conc in the genion

On Thu, Aug 11, 2011 at 11:35 PM, Tsjerk Wassenaar wrote: > Hi, > >>> I'd be amazed if the error was in the code and not in your calculation. The >>> number of water molecules doesn't matter for the calculation of the ion >>> concentration, of course. Pay attention to your box shape. And do consid

Re: [gmx-users] how to calculate the conc in the genion

Hi, >> I'd be amazed if the error was in the code and not in your calculation. The >> number of water molecules doesn't matter for the calculation of the ion >> concentration, of course. Pay attention to your box shape. And do consider >> the number of ions has to be an integer, so for a given vol

[gmx-users] RE: gmx-users Digest, Vol 88, Issue 65

Thank Mark, I will try your suggestions. Stephane Message: 4 Date: Fri, 12 Aug 2011 00:31:46 +1000 From: Mark Abraham Subject: Re: [gmx-users] Use different fudgeLJ and fudgeQQ values in simulations with the AMBER force field To: Discussion list for GROMACS users Message-ID: <4e43e7d2.

[gmx-users] reg genion

Dear justin,   Thank you for your previous mail   I am using genion pro gramme  if i use genion programme using random option in number of times Then will it add positive and negative ions in  different (xyz) coordinate in every time otherwise will it show same

Re: [gmx-users] how to calculate the conc in the genion

On Thu, Aug 11, 2011 at 10:41 PM, Mark Abraham wrote: > On 12/08/2011 12:37 AM, lina wrote: >> >> Hi, >> >> after using genion -conc 0.1 >> >> certain number of Na and Cl were added in solvent. >> >> but when I tried to calculate back, namely, based on the number of Na >> and Cl, the number of wat

[gmx-users] PCA and Free energy landscape

Hello, I have done PCA using cartesian coordinates by the help of gromacs(g_covar and g_anaeig), then using the 2-d projection of trajectory on first two eigenvectors as reaction coordinates,I have calculated a 2-d representation of the gibbs free energy landscape(g_sham) using gromacs.Now on this

Re: [gmx-users] How to install gromacs 4.5.1

cd /usr/lib (or locate libfftw3.so.3.2.4) you may notice the /usr/lib/libfftw3.so.3.2.4 make a link, sudo ln -sf /usr/lib/libfftw3.so.3.2.4 /usr/lib/libfftw3.so.3 then shall be no problem. On Thu, Aug 11, 2011 at 10:50 PM, Mark Abraham wrote: > On 12/08/2011 12:38 AM, afsaneh maleki wrote: >

[gmx-users] vsites with NAC and opls

This is fixed, just posting for posterity. If one wants to run pdb2gmx with -vsites hydrogens on gromacs 4.5.4 or 4.0.7 while using the oplss ff, there is the error message: Fatal error: Can't find dummy mass for type opls_242 bonded to type opls_238 in the virtual site database (.vsd files

Re: [gmx-users] How to install gromacs 4.5.1

On 12/08/2011 12:38 AM, afsaneh maleki wrote: Hi, My characteristics computer: Root at ...fftw-3.2.2]# uname -a Linux localhost.localdomain 2.6.31.5-127.fc12.i686.PAE #1 SMP Sat Nov 7 21:25:57 EST 2009 i686 i686 i386 GNU/Linux To install FFTW version 3.2.2. I used the following commands:

Re: [gmx-users] how to calculate the conc in the genion

On 12/08/2011 12:37 AM, lina wrote: Hi, after using genion -conc 0.1 certain number of Na and Cl were added in solvent. but when I tried to calculate back, namely, based on the number of Na and Cl, the number of water molecular and the box volumn, but seems can't come back, I mean, can't obtai

Re: [gmx-users] Re: -dt option in g_velacc

On 12/08/2011 12:30 AM, Jinan Niu wrote: On 8/08/2011 11:08 PM, Mark Abraham wrote: >I don't quite follow your question, but for correlation functions to be >computed accurately, you need data collected much more frequently >than >the relevant time scales. That can require good planning. >Mark H

[gmx-users] How to install gromacs 4.5.1

Hi, My characteristics computer: Root at …fftw-3.2.2]# uname -a Linux localhost.localdomain 2.6.31.5-127.fc12.i686.PAE #1 SMP Sat Nov 7 21:25:57 EST 2009 i686 i686 i386 GNU/Linux To install FFTW version 3.2.2. I used the following commands: Root at …fftw-3.2.2]# ./configure --enable-thr

[gmx-users] how to calculate the conc in the genion

Hi, after using genion -conc 0.1 certain number of Na and Cl were added in solvent. but when I tried to calculate back, namely, based on the number of Na and Cl, the number of water molecular and the box volumn, but seems can't come back, I mean, can't obtain the result of 0.1mol/L. I read the

Re: [gmx-users] strange vdw energy from rerun with GBSA model.

Hello Please see my response below. On Thu, Aug 11, 2011 at 10:23 AM, Mark Abraham wrote: > On 11/08/2011 10:22 PM, Da-Wei Li wrote: > > Dear Mark and others > > I did more tests and thought that it might come from numerical error. The > reasons are > > 1. If I use .trr file instead of the low

Re: [gmx-users] Use different fudgeLJ and fudgeQQ values in simulations with the AMBER force field

On 12/08/2011 12:16 AM, intra\sa175950 wrote: Dear All, Few years ago, C. Neale (thanks to him!) posted in the GROMACS mailing list a very useful tutorial [1] to scale the Coulombic 1-4 interactions when we combine forcefields with different fudgeLJ and fudgeQQ values. I am trying to apply t

[gmx-users] Re: -dt option in g_velacc

On 8/08/2011 11:08 PM, Mark Abraham wrote: >I don't quite follow your question, but for correlation functions to be >computed accurately, you need data collected much more frequently >than >the relevant time scales. That can require good planning. >Mark Hi,Mark and other gmx users： when I used g_

[gmx-users] Use different fudgeLJ and fudgeQQ values in simulations with the AMBER force field

Dear All, Few years ago, C. Neale (thanks to him!) posted in the GROMACS mailing list a very useful tutorial [1] to scale the Coulombic 1-4 interactions when we combine forcefields with different fudgeLJ and fudgeQQ values. I am trying to apply this trick to a system containing a peptide and a

Re: [gmx-users] Re: VMD_PLUGIN_PATH

On 11/08/2011 11:02 PM, PAUL NEWMAN wrote: Dear Mark, Thanks for replying. Yes I am using bash. Yes the bash recognize the set path. When I do echo, I got the follwoing echo $VMD_PLUGIN_PATH /home/pet/vmd/1.9/plugins/molfile What can be wrong? Maybe the program is not in this folder? Which

Re: [gmx-users] strange vdw energy from rerun with GBSA model.

On 11/08/2011 10:22 PM, Da-Wei Li wrote: Dear Mark and others I did more tests and thought that it might come from numerical error. The reasons are 1. If I use .trr file instead of the low precision xtc file, things become better, ie, I get much less snapshots that has high energy. That do

[gmx-users] Regarding parametrisation

Dear Justin, I was reading one of your literature on building GROMOS-compatible small molecule topologies. I was trying to reproduce the AM1BCC partial charges for the p-cresol using Antechamber from amber tools version 1.5. I will enlist what I have got and with literature values

Re: [gmx-users] Trouble installing mdrun-gpu from gromacs 4.5.4 package

Hi! Maybe you have to install a missing packages, libxml2 and CUDA? 2011/8/11 Micholas Smith : > (My apologizes for the double post, my mail client apparently sent my > previous email as html, so here is a clean re-print) > > Hello, > > After undergoing a fresh installation of Gromacs 4.5.4, I st

Re: [gmx-users] How to install FFTW 3.2.2

afsaneh maleki wrote: Hi, To compile a single-precision version of the libraries and install FFTW version 3.2. I followed the steps inhttp://www.gromacs.org/Downloads/Installation_Instructions#Prerequisites . my

Re: [gmx-users] strange vdw energy from rerun with GBSA model.

Dear Justin You are right about the cut-off. The vdw energy spike disappeared after I increased the cut-off in the rerun. But I still don't understand why? Can the cutoff error build up to several thousand kj/mol for 100AA protein. Again I would like to emphasize NOT to use a xtc file in MM/PBSA

Re: [gmx-users] Trouble installing mdrun-gpu from gromacs 4.5.4 package

Micholas Smith wrote: (My apologizes for the double post, my mail client apparently sent my previous email as html, so here is a clean re-print) Hello, After undergoing a fresh installation of Gromacs 4.5.4, I still can't seem to get the mdrun-gpu program to compile and install. In order to

[gmx-users] How to install FFTW 3.2.2

Hi, To compile a single-precision version of the libraries and install FFTW version 3.2. I followed the steps inhttp:// www.gromacs.org/Downloads/Installation_Instructions#Prerequisites . my computer characteristics: Root at …fftw-3.2.2]# uname -a Linux localhost.localdomain 2.6.31.5-127.fc12.i

[gmx-users] Trouble installing mdrun-gpu from gromacs 4.5.4 package

(My apologizes for the double post, my mail client apparently sent my previous email as html, so here is a clean re-print) Hello, After undergoing a fresh installation of Gromacs 4.5.4, I still can't seem to get the mdrun-gpu program to compile and install. In order to get the original package

Re: [gmx-users] strange vdw energy from rerun with GBSA model.

Da-Wei Li wrote: Dear Justin An implicit water simulaiton with this short cutoff is problematic but I think it is fine for rerun. I want to exactly repeat the original energies in the explicit water MD. The manu say "neighbor list searching will be performed for every frame" with rerun op

[gmx-users] Re: VMD_PLUGIN_PATH

Dear Mark, Thanks for replying. Yes I am using bash. Yes the bash recognize the set path. When I do echo, I got the follwoing echo $VMD_PLUGIN_PATH /home/pet/vmd/1.9/plugins/molfile What can be wrong? Maybe the program is not in this folder? Which program is searching for this pluging Thanks f

Re: [gmx-users] strange vdw energy from rerun with GBSA model.

Dear Justin An implicit water simulaiton with this short cutoff is problematic but I think it is fine for rerun. I want to exactly repeat the original energies in the explicit water MD. The manu say "neighbor list searching will be performed for every frame" with rerun option. So that I don't thi

[gmx-users] Constraints not working in pull code (sometimes, sometimes not)

Dear Krapnik: 1. please make the test cases identical, that means doing a simulation that you may not really be interested in so that the solutes are the same for both lipid and octane. It also means setting the displacements to similar values in my opinion (because perhaps the problem is

Re: [gmx-users] strange vdw energy from rerun with GBSA model.

Da-Wei Li wrote: Dear Mark and others I did more tests and thought that it might come from numerical error. The reasons are 1. If I use .trr file instead of the low precision xtc file, things become better, ie, I get much less snapshots that has high energy. 2. I supplied -pforce in my m

Re: [gmx-users] pmf_calculation

shahid nayeem wrote: Both files hist.xvg and profile.xvg both are simultaneous output of this command. I did not run it twice, once to get profile.xvg and then to get hist.xvg as you uderstood. They cannot be simultaneous output. The file named "hist.xvg" contains a PMF profile and has a

Re: [gmx-users] pmf_calculation

Both files hist.xvg and profile.xvg both are simultaneous output of this command. I did not run it twice, once to get profile.xvg and then to get hist.xvg as you uderstood. On Thu, Aug 11, 2011 at 5:42 PM, Justin A. Lemkul wrote: > > > shahid nayeem wrote: > >> I used following command >> g_wham

Re: [gmx-users] strange vdw energy from rerun with GBSA model.

Dear Mark and others I did more tests and thought that it might come from numerical error. The reasons are 1. If I use .trr file instead of the low precision xtc file, things become better, ie, I get much less snapshots that has high energy. 2. I supplied -pforce in my mdrun -rerun and found tha

Re: [gmx-users] pmf_calculation

shahid nayeem wrote: I used following command g_wham_4.5.4 -it tpr-files.dat -if pullf-files.dat -o hist -unit kCal Both profile.xvg and hist.xvg are created with this command using same pullf.xvg and .tpr files. An identical command with identical input files producing totally different o

Re: [gmx-users] pmf_calculation

I used following command g_wham_4.5.4 -it tpr-files.dat -if pullf-files.dat -o hist -unit kCal Both profile.xvg and hist.xvg are created with this command using same pullf.xvg and .tpr files. shahid Nayeem On Thu, Aug 11, 2011 at 5:07 PM, Justin A. Lemkul wrote: > > > shahid nayeem wrote: > >>

[gmx-users] Re: A very good morning Sir

Please keep all Gromacs-related correspondence on the gmx-users list. I am not a private tutor. I am CC'ing this message to the list and would ask that all further discussion be posted there. Comments embedded below. Sabitoj Singh Virk wrote: Hello, It could be really helpful of a perso

Re: [gmx-users] pmf_calculation

shahid nayeem wrote: Dear Justin I did some more sampling and sending you profile.xvg, histo.xvg. and hist.xvg. I am sending histo.xvg hist.xvg and profile.xvg. please tell my the difference in profile.xvg and hist.xvg. Both should be same but I get different curves here. I can't tell yo

Re: [gmx-users] Topology for a new ligand

Kavyashree M wrote: Dear gromacs users, I wanted to know the steps to be followed in order to generate a topology for a new ligand. I went through the mailing list and http://www.gromacs.org/Documentation/How-tos/Parameterization but was not clear. All force fields are different, and since

[gmx-users] Topology for a new ligand

Dear gromacs users, I wanted to know the steps to be followed in order to generate a topology for a new ligand. I went through the mailing list and http://www.gromacs.org/Documentation/How-tos/Parameterization but was not clear. Awaiting your suggestions Thanking you With regards M. Kavyashree -

Re: [gmx-users] secondary structure propensities of residues

On 10/08/2011 6:03 AM, César Ávila wrote: Hi, I downloaded release-4-5-patches from git. It compiles and installs successfully. Nevertheless I am getting a segmentation fault. Are you using a version of DSSP that is compatible with GROMACS, pre previous discussion of DSSP changes? Mark Wi

Re: [gmx-users] VMD_PLUGIN_PATH

On 10/08/2011 1:21 PM, PAUL NEWMAN wrote: Hi Gromacs Users, I am using the gromacs analysing tools to analyze my DCD file produced by NAMD. I set up the VMD_PLUGIN_PATH before running however I got the error that the VMD_PLUGIN_PATH was not set up. Can anyone give me a hand? Please see below

Re: [gmx-users] strange vdw energy from rerun with GBSA model.

On 11/08/2011 1:45 AM, Da-Wei Li wrote: Dear Mark Could you please help me out? I can send you the trajectory (1000 snapshot in pdb format), mdp, topol file. I use Gromacs-4.5.3. Not unless you can show me a shell script and .mdp file that can take your original trajectory, do my suggested p

Re: [gmx-users] Selenomethionine in pdb file

On 11/08/2011 2:10 PM, R.Vidya Rajendran (10PHD013) wrote: Hello Friends, I would like to do simulation of a protein containing 'selenomethionine' [MSE] in coordinate file, during the first step of pdb2gmx this residue is not recognizing by any of the force field and getting fatal error 'Residue

Re: [gmx-users] Arginine_Hydrochloride topology

On 11/08/2011 7:24 PM, shahid nayeem wrote: Hi Justin I prepared a box of SOL and arginine Hydrochloride. But when I solvate my protein with this box now the positively charged arginine is as solvent and this causes problem in grompp. It gives error like "No such Molecule types ARG" etc. Solva

Re: [gmx-users] Arginine_Hydrochloride topology

Hi Justin I prepared a box of SOL and arginine Hydrochloride. But when I solvate my protein with this box now the positively charged arginine is as solvent and this causes problem in grompp. It gives error like "No such Molecule types ARG" etc. Solvating arginine with water and preparing a box was

[gmx-users] Re: Constraints not working in pull code (sometimes, sometimes not)

Dear Justin Thank you for your responses, but it still is not clear to me why is that happening > I don't see any real problem here. The DOPC membrane probably holds its shape > better than the octanol slab and thus the reference position (which determines > the constraint) is less mobile. That