[gmx-users] Chemical Potential

Dear Gmx Users, I am wondering whether it is possible to obtain in Gromacs chemical potential e.g. of water in the protein - ligand system? Please, advise me to do some further reading, suggest method, maybe tutorial? Thank you, Steven -- gmx-users mailing listgmx-users@gromacs.org http://l

Re: [gmx-users] mdrun-gpu error

Mark, THe normal mdrun also hangs thus not generating any output. On Thu, Jan 19, 2012 at 3:09 AM, Mark Abraham wrote: > On 19/01/2012 2:59 AM, aiswarya.pa...@gmail.com wrote: > > Hi, > > Its going into the running mode but gets hang there for long hours which > generating any data in the outp

Re: [gmx-users] getting rid of PBC, completely

On Thu, Jan 19, 2012 at 12:17 PM, Mark Abraham wrote: > On 19/01/2012 5:39 PM, Chandan Choudhury wrote: > >> >> Dear gmx-users, >> >> I have a simulated a system containing a linear polymer in a cubic box >> with water molecules. I need to get rid of PBC effect on the system such >> that I can ex

Re: [gmx-users] getting rid of PBC, completely

Hi Chandan, The box is accessible from the t_trxframe struct. Assuming you have t_trxframe *fr You can access it through fr->box But if you remove jumps first, you're fine anyway. Just don't put things back in the box afterwards. And don't center if your aim is calculating MSDs. Hope it helps

[gmx-users] Chemical Potential

Does anyone can help? Dear Gmx Users, I am wondering whether it is possible to obtain in Gromacs chemical potential e.g. of water in the protein - ligand system? Please, advise me to do some further reading, suggest method, maybe tutorial? Thank you, Steven -- gmx-users mailing listgmx-

Re: [gmx-users] Chemical Potential

On 01/19/2012 11:34 AM, Steven Neumann wrote: Does anyone can help? Dear Gmx Users, I am wondering whether it is possible to obtain in Gromacs chemical potential e.g. of water in the protein - ligand system? Please, advise me to do some further reading, suggest method, maybe tutorial? Thank yo

Re: [gmx-users] Chemical Potential

On 2012-01-19 14:49, Ivan Gladich wrote: On 01/19/2012 11:34 AM, Steven Neumann wrote: Does anyone can help? Dear Gmx Users, I am wondering whether it is possible to obtain in Gromacs chemical potential e.g. of water in the protein - ligand system? Please, advise me to do some further reading, s

Re: [gmx-users] Chemical Potential

Hi, If I understand the question correctly, you want to know the water chemical potential in the water/protein/ligand system. If so, in principle it should be possible to approximate the water chemical potential using test particle insertion. Gromacs has a utility for that. Cheers, René ===

Re: [gmx-users] mdrun-gpu error

On 19/01/2012 8:45 PM, aiswarya pawar wrote: Mark, THe normal mdrun also hangs thus not generating any output. OK. It's your problem to solve... keep simplifying stuff until you can isolate a small number of possible causes. Top of the list is file system availability. Mark On Thu, Jan

Re: [gmx-users] getting rid of PBC, completely

On Thu, Jan 19, 2012 at 3:49 PM, Tsjerk Wassenaar wrote: > Hi Chandan, > > The box is accessible from the t_trxframe struct. Assuming you have > > t_trxframe *fr > > You can access it through > > fr->box > Thanks Tsjerk. It (fr.box) did help me to get the box coordinates. fr.box[XX][XX], fr.box

Re: [gmx-users] getting rid of PBC, completely

Hi Chandan, > fr.box[XX][XX], fr.box[YY][YY] and fr.box[ZZ][ZZ] gives me the values > but fr.box[XX][YY], fr.box[XX][ZZ] prints 0. Which seems to me that the > origin of the box is at (0,0,0). Then,  fr.box[XX][XX] is the maximum > X-coordinate, fr.box[YY][YY] is the maximum Y-coordinate,fr.box[ZZ

Re: [gmx-users] getting rid of PBC, completely

On 19/01/2012 11:27 PM, Chandan Choudhury wrote: On Thu, Jan 19, 2012 at 3:49 PM, Tsjerk Wassenaar > wrote: Hi Chandan, The box is accessible from the t_trxframe struct. Assuming you have t_trxframe *fr You can access it through fr->box Thanks

[gmx-users] pdb2gmx -ter with cyclic peptide

Hi there, normally to generate a cyclic peptide I use to edit specbond.dat to force the bond between the N- and C-termini and I use the -ter flag into pdb2gmx tool in order to avoid to add hydrogens and oxygen to the end of the peptide. This was okay until the gromacs version 4.0.5 with opls ff.

Re: [gmx-users] Chemical Potential

Thank you very much guys! I will search for some reading. If you can suggest a tutorial I will appreciate. On Thu, Jan 19, 2012 at 11:57 AM, René Pool wrote: > Hi, > > If I understand the question correctly, you want to know the water > chemical potential in the water/protein/ligand system. > If

[gmx-users] Residue representation

Dear Gmx Users, I am simulating (Charmm27 ff) my protein in presence of a tube (made of atoms). This tube is a representation of a surface of protein. I want to do an approximation of residues on the surface. I divided amino acids and represent them as: - positively charged - I used Na+ [ SOD ] [

Re: [gmx-users] mdrun-gpu error

And sorting out where the /bin/cat error comes from because that is surely not a Gromacs message! Cheers, -- Szilárd On Thu, Jan 19, 2012 at 1:12 PM, Mark Abraham wrote: > On 19/01/2012 8:45 PM, aiswarya pawar wrote: > > Mark, > > THe normal mdrun also hangs thus not generating any output. > >

Re: [gmx-users] mdrun-gpu error

Has the tesla card got to do anything with the error. Am using Nvidia Tesla S1070 1U server. On Thu, Jan 19, 2012 at 8:37 PM, Szilárd Páll wrote: > And sorting out where the /bin/cat error comes from because that is > surely not a Gromacs message! > > Cheers, > -- > Szilárd > > > > On Thu, Jan 1

Re: [gmx-users] mdrun-gpu error

when i tired running it again, i got an error as Cuda error in file '/home/staff/sec/secdpal/software/openmm_tesla/platforms/cuda/./src/kernels// bbsort.cu' in line 176 : unspecified launch failure. /bin/cat: file_loc: No such file or directory On Thu, Jan 19, 2012 at 8:45 PM, aiswarya pawar wrot

[gmx-users] Problem with Position Restraints (before running SMD)!

Hi guys, When I did my SMD simulation by applying load to a certain group of atoms and fixing certain atoms by modifying the topology file, the points that i have fixed moved from there original position. I don't know what the problem is! Any suggestion! To make what I was doing clear, I st

Re: [gmx-users] Problem with Position Restraints (before running SMD)!

Talal E. AlOtaibi wrote: Hi guys, When I did my SMD simulation by applying load to a certain group of atoms and fixing certain atoms by modifying the topology file, the points that i have fixed moved from there original position. I don't know what the problem is! Any suggestion! Posi

Re: [gmx-users] Problem with Position Restraints (before running SMD)!

Talal E. AlOtaibi wrote: ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 13301 1000 1000 1000 14261 1000 1000 1000 14371 1000

[gmx-users] How to find Hbonding partner

Hi,    I am wondering whether there is any way in GROMACS that one can find which groups are the main Hbonding partners in a trajectory. For example, if I simulate a peptide in water, I want to know during the simulation, which particular atoms in the peptides are making most of the Hbonds with

[gmx-users] writing checkpoints

We are running quite a large system with a default checkpoint intervals (15 minutes). However, in the md.log file, it is written like below Writing checkpoint, step 138 at Thu Jan 19 11:00:36 2012 Writing checkpoint, step 1380010 at Thu Jan 19 11:00:41 2012 Writing checkpoint, step 1380020 at

Re: [gmx-users] mdrun-gpu error

That's a generic GPU kernel launch failure which can mean anything, from faulty hardware to bad driver to messed up installation. Does the memory test run? Try to compile/install again and see if it works. -- Szilárd On Thu, Jan 19, 2012 at 4:18 PM, aiswarya pawar wrote: > when i tired runnin

Re: [gmx-users] mdrun-gpu error

Szilárd, I did a memory test run yesterday and it went fine but today received an error. So you mean to say the tesla card version nothing to do with this right. Thanks On Thu, Jan 19, 2012 at 11:09 PM, Szilárd Páll wrote: > That's a generic GPU kernel launch failure which can mean anything, >

Re: [gmx-users] How to find Hbonding partner

Sanku M wrote: Hi, I am wondering whether there is any way in GROMACS that one can find which groups are the main Hbonding partners in a trajectory. For example, if I simulate a peptide in water, I want to know during the simulation, which particular atoms in the peptides are making most

Re: [gmx-users] mdrun-gpu error

aiswarya pawar wrote: Szilárd, I did a memory test run yesterday and it went fine but today received an error. So you mean to say the tesla card version nothing to do with this right. You're trying to solve multiple problems at once. You told Mark that the normal mdrun executable (whic

[gmx-users] Reg: Number of nodes in REMD

Hi there, I am trying to run REMD using the following command mdrun_mpi -s run_.tpr -multi 8 -replex 100 and i am getting the following error Fatal error: The number of nodes (1) is not a multiple of the number of simulations (8) i tried using -np option to give the number of nodes but it is

Re: [gmx-users] Reg: Number of nodes in REMD

Rohit Farmer wrote: Hi there, I am trying to run REMD using the following command mdrun_mpi -s run_.tpr -multi 8 -replex 100 and i am getting the following error Fatal error: The number of nodes (1) is not a multiple of the number of simulations (8) i tried using -np option to give the nu

Re: [gmx-users] Problem with Position Restraints (before running SMD)!

Talal E. AlOtaibi wrote: Thank you so much Justin, I made some changes and the SMD run was fine with no errors but I still have the same problem (the fixed points moved away from their original position). How great is the displacement? Recall what I said before - position restraints a

[gmx-users] sudden jumps in RMSD etc.

Hi all, I am doing duplicate MD simulations with a protein-ligand system. After processing one trajectory by trjconv with the optioin -pbc nojump, I still find abrupt jumps (on the scale of nm) in RMSDs and COM distances. Then I tried -pbc mol -ur compact, which did not work. And then -fit progr

[gmx-users] query on g_sorient

Hi,   I am trying to understand what are the angles g_sorient plans to compute.  The manual says that the theta1 is "the angle with the vector from the first atom of the solvent molecule to the midpoint between atoms 2 and 3" .  But, I wonder what is the reference position of this angle  ? In ot

Re: [gmx-users] sudden jumps in RMSD etc.

On 20/01/2012 7:55 AM, Yun Shi wrote: Hi all, I am doing duplicate MD simulations with a protein-ligand system. After processing one trajectory by trjconv with the optioin -pbc nojump, I still find abrupt jumps (on the scale of nm) in RMSDs and COM distances. Then I tried -pbc mol -ur compa

Re: [gmx-users] query on g_sorient

Sanku M wrote: Hi, I am trying to understand what are the angles g_sorient plans to compute. The manual says that the theta1 is "the angle with the vector from the first atom of the solvent molecule to the midpoint between atoms 2 and 3" . But, I wonder what is the reference position of

[gmx-users] Lincs warnings

Hi all, I've been working on some structures between 2.5A and 3.4A in resolution and all of my structures suffer from lincs warnings. >From reading the page about lincs warnings, I've performed a more lengthy equilibration: I'm using gromacs 4.0.7 single precision and the G53a6 force field with s

Re: [gmx-users] Lincs warnings

On 20/01/12, Ben Porebski wrote: > Hi all, > > > I've been working on some structures between 2.5A and 3.4A in resolution and > all of my structures suffer from lincs warnings. > From reading the page about lincs warnings, I've performed a more lengthy > equilibration: > > > I'm using grom

Re: [gmx-users] mdrun-gpu error

Justin, Sorry for not giving the correct information. Gromacs version 4.5.5 Tesla card- Nvidia Tesla S1070 (Tesla T10 Processor) Cuda version 3.1 CMake 2.8 I installed the OpenMM from the source using commands= ccmake -i . make make test make install everything went fine and set the paths exp

[gmx-users] Regarding ngmx with double precision

Dear All, While installing Gromacs in double precision, I am not able to make ngmx run. Is it because of lack of X libraries. I want to run ngmx trajectory viewer. So I kindly request you to suggest me to make ngmx run. Thank you in Advance *With Regards, Ravi Kumar Venkatraman, IPC

[gmx-users] How to balance charge for modeling N2 molecules

Hi, I asked this question before. Thanks to Justin, he did reply as follows. Kiwoong Kim wrote: Hi, I'm getting better to use Gromacs owing to many posts on this sites :) . I have several questions about adding the counter-ions. My system has a number of N2 molecules which has charge, -0.404

Re: [gmx-users] Regarding ngmx with double precision

On 20/01/2012 5:05 PM, Ravi Kumar Venkatraman wrote: Dear All, While installing Gromacs in double precision, I am not able to make ngmx run. Is it because of lack of X libraries. I want to run ngmx trajectory viewer. So I kindly request you to suggest me to make ngmx run. You n

Re: [gmx-users] How to balance charge for modeling N2 molecules

On 20/01/2012 5:51 PM, Kiwoong Kim wrote: Hi, I asked this question before. Thanks to Justin, he did reply as follows. Kiwoong Kim wrote: Hi, I'm getting better to use Gromacs owing to many posts on this sites :) . I have several questions about adding the counter-ions. My