[gmx-users] regarding simulation of peptide and protein complex

Hello everyone.. I have 2 do the simulation of protein and peptide complex.I want to ask as for protein and ligand complex we have 2 create topology of ligand using prodrg sever mostly.Now if ligand is peptide then I have 2 build the topology of peptide using pdb2gx or anyother means?Looking forw

[gmx-users] Re: [gmx-developers] implicit solvent

晓英 wrote: Dear developers, I'm doing implicit solvent in gromacs 4.5.2 with amber03 force field but it appears some problem. I have done energy minimization .Then mdrun in NVT,but there is always LINCS error .When I make impolicit_solvent=no,it can run successfully. I have send a email to

Re: [gmx-users] maintained an Hbond using a distance restraint

Thanks! Itamar. On 14/07/11 11:53 AM, Justin A. Lemkul wrote: Itamar Kass wrote: Hi Justin, Thanks for the quick replay. Regrading Q.1 that was my idea, just wanted to be sure. Regarding Q.2, I think a more relevant phrase would be, how big a force I can use without cancel the "validity'

Re: [gmx-users] maintained an Hbond using a distance restraint

Itamar Kass wrote: Hi Justin, Thanks for the quick replay. Regrading Q.1 that was my idea, just wanted to be sure. Regarding Q.2, I think a more relevant phrase would be, how big a force I can use without cancel the "validity' of my simulations? I still can't say whether there is a direc

Re: [gmx-users] maintained an Hbond using a distance restraint

Hi Justin, Thanks for the quick replay. Regrading Q.1 that was my idea, just wanted to be sure. Regarding Q.2, I think a more relevant phrase would be, how big a force I can use without cancel the "validity' of my simulations? In addition, just to make it clear for myself, when I use 2 for ty

Re: [gmx-users] maintained an Hbond using a distance restraint

Itamar Kass wrote: Hi, I wish to force my system to maintained an Hbond during a simulation. In order to do so I am using a distance restraint protocol, with the following parameters: In the topology file/: /[ distance_restraints ] ; ai aj type index type' low up1 up2 fac 2786 326

[gmx-users] maintained an Hbond using a distance restraint

Hi, I wish to force my system to maintained an Hbond during a simulation. In order to do so I am using a distance restraint protocol, with the following parameters: In the topology file/: /[ distance_restraints ] ; ai aj type index type' low up1 up2 fac 2786 3262 10 2 0.295

Re: [gmx-users] R: Re: rhombic dodecahedron and g_sas

On 14/07/2011 1:08 AM, Anna Marabotti wrote: In any case, if I understand well, I have to convert my .gro file (into a .tpr file to obtain the exact value of hydrophobicity/hydrophilicity, right? You should be able to use the .tpr which which you generated the trajectory. One doesn't "convert"

[gmx-users] g_dipoles -slab option

Hi all, I am testing g_dipoles tool in GROMACS with a simple system containing only tip3p water molecules in a cubic box (6X6X6nm) with periodic boundary conditions in xyz. After the simulation is finished, using g_dipoles, I get the average epsilon=99.776 and the epsilon vs times also indicate th

Re: Re : Re : [gmx-users] Re: Adding Ions

errabah fatima ezzahra wrote: you mean that i should have it as protein and Ions but no water No. Please read what I said in the last message (it was likely exactly what you needed) and do some basic tutorial material if these concepts are unfamiliar to you. You can't leave parts of you

Re : Re : [gmx-users] Re: Adding Ions

you mean that i should have it as protein and Ions but no water tc-grps = Protein ions tau_t = 0.1 0.1 ref_t = 300 300 De : Justin A. Lemkul À : Discussion list for GROMACS users Envoyé le : Mercredi 13 Juillet 2011 14h42 Ob

Re: [gmx-users] Recommended parameters for NVE simulation of SPCE water

Andrew DeYoung wrote: Hi, I am a Gromacs novice and am trying to simulate 1000 SPC/E water molecules (with the usual charges) in the NVE ensemble. I am trying to obtain good energy conservation. My configuration contains a 10-by-10-by-10 cubic crystal of SPC/E waters, with a lattice constan

Re: [gmx-users] Slab Ewald test

Alex Marshall wrote: Hi all, I'm currently trying to run a simple test on how electrostatics are handled in gromacs when the slab Ewald summation is used. My system consists of 26 point charges, with 25 arranged in a square lattice in the XY plane and the 26th above the charge in the middle

Re: Re : Re : [gmx-users] Re: Adding Ions

errabah fatima ezzahra wrote: I am trying to do energy minimization but * grompp -f em.mdp -c waterbox_ions.gro -p file.top -o em.tpr * mdrun -v -s em.tpr -c system.gro the waterbox_ions.gro have the NA ions but when i check the system.gro it doe

[gmx-users] Slab Ewald test

Hi all, I'm currently trying to run a simple test on how electrostatics are handled in gromacs when the slab Ewald summation is used. My system consists of 26 point charges, with 25 arranged in a square lattice in the XY plane and the 26th above the charge in the middle. My goal is to calculate th

Re : Re : [gmx-users] Re: Adding Ions

I am trying to do energy minimization but * grompp -f em.mdp -c waterbox_ions.gro-p file.top -o em.tpr * mdrun -v -s em.tpr -c system.grothe  waterbox_ions.gro have the NA ions but when i check the system.gro it does not have the ions what am i doing wrong here?? ___

Re: Re : [gmx-users] Re: Adding Ions

errabah fatima ezzahra wrote: *I am trying to do a Short position restrained simulation so i wrote * grompp -f pr.mdp -c system.gro -p file.top -o file.tpr , i added the NA+ to the pr.mdp file here the pr.mdp tc-grps = Protein WNA+ First of all, you should never do this.

Re : [gmx-users] Re: Adding Ions

I am trying to do a Short position restrained simulation so i wrote  grompp -f pr.mdp -c system.gro-p file.top -o file.tpr , i added the NA+ to the pr.mdp file here the pr.mdp tc-grps =  Protein  W    NA+ tau_t   =  0.1  0.1  0.1 ref_t   =  300  300

[gmx-users] Recommended parameters for NVE simulation of SPCE water

Hi, I am a Gromacs novice and am trying to simulate 1000 SPC/E water molecules (with the usual charges) in the NVE ensemble. I am trying to obtain good energy conservation. My configuration contains a 10-by-10-by-10 cubic crystal of SPC/E waters, with a lattice constant of approximately 4.7 Angs

[gmx-users] Re: Adding Ions

errabah fatima ezzahra wrote: Hi Justin when i seperated the NA+ and 6 i got this error NOTE 1 [file em.mdp]: For energy conservation with switch/shift potentials, rlist should be 0.1 to 0.3 nm larger than rcoulomb. NOTE 2 [file em.mdp]: For energy conservation with switch/shift poten

[gmx-users] Adding Ions

Hi Justin when i seperated the NA+ and 6 i got this error NOTE 1 [file em.mdp]:   For energy conservation with switch/shift potentials, rlist should be 0.1   to 0.3 nm larger than rcoulomb. NOTE 2 [file em.mdp]:   For energy conservation with switch/shift potentials, rlist should be 0.1   to

Re: [gmx-users] Segmentation fault

Sayan Bagchi wrote: Hello All, I was trying to run a MD simulation of a 17 amino acid peptide. At the position restraint step, the program crashed after running ~536 ps. It gave the error message: "t=536.242 ps: Water molecule starting at atom 6101 cannot be settled. Check for bad contacts

[gmx-users] Segmentation fault

Hello All, I was trying to run a MD simulation of a 17 amino acid peptide. At the position restraint step, the program crashed after running ~536 ps. It gave the error message: "t=536.242 ps: Water molecule starting at atom 6101 cannot be settled. Check for bad contacts and/or reduce the timeste

Re: Re : Re : [gmx-users] Adding Ions

errabah fatima ezzahra wrote: I actually getting that error to number of coordinates in coordinate file (waterbox_ions.gro, 3797) does not match topology (1pef.top, 3791) Please make sure to state up front exactly what errors you're receiving. I suspect, then, that my statem

Re : Re : [gmx-users] Adding Ions

I actually getting that error to number of coordinates in coordinate file (waterbox_ions.gro, 3797) does not match topology (1pef.top, 3791) De : Justin A. Lemkul À : Discussion list for GROMACS users Envoyé le : Mercredi 13 Juillet 2011 13h49 Ob

Re: Re : [gmx-users] Adding Ions

Justin A. Lemkul wrote: errabah fatima ezzahra wrote: i added the NA using the genion * genion -s em.tpr -o waterbox_ions.gro -np 6 , and i added the NA to the topology file , subtracted the water number by 6. tail waterbox_ions.gro file have this 3567WW 3789 1.256

Re: Re : [gmx-users] Adding Ions

errabah fatima ezzahra wrote: i added the NA using the genion * genion -s em.tpr -o waterbox_ions.gro -np 6 , and i added the NA to the topology file , subtracted the water number by 6. tail waterbox_ions.gro file have this 3567WW 3789 1.256 3.600 3.784 3568W

Re : [gmx-users] Adding Ions

i added the NA using the genion  * genion -s em.tpr -o waterbox_ions.gro -np 6, and i added the NA to the topology file , subtracted the water number by 6. tail waterbox_ions.grofile have this  3567W    W 3789   1.256   3.600   3.784  3568W    W 3790   2.491   6.539   2.34

Re: [gmx-users] reg electrostatics

vidhya sankar wrote: Dear justin Thank you for previous patient reply To study the salt effect (ionc strength) on H-bonding of protein Which option of Electrstatics is best either PME or Cut-off ? Because when i read one recent articles They used Cut-off option I T

[gmx-users] reg electrostatics

Dear justin Thank you for previous patient reply      To study the salt effect  (ionc strength) on H-bonding of protein Which option of Electrstatics is best either PME or Cut-off ? Because when i read one recent  articles They used Cut-off option I Think PME is recent option

Re: [gmx-users] Adding Ions

errabah fatima ezzahra wrote: Hi All, I have a peptide that has three positive charged amino acids (LYS) and four negative charged amino acids (GLU) consequently it is a negative peptide. is that right Assuming typical protonation states, and further assuming that there are no other un

Re: Res: Res: [gmx-users] Topology for nBuOH

Juliana Angeiras wrote: Hi Justin, Sorry if I am slow to understand these things, but I really want to use gromacs for simulate my system: butanol-water mixture in several concentrations, using tip3p for water and include the parameters for butanol and for water-butanol intermolecular inte

[gmx-users] Adding Ions

Hi All, I have a peptide that has three positive charged amino acids  (LYS) and four negative charged amino acids (GLU) consequently it is a negative peptide. is that right when i run gromacs simualtion grompp DOES NOT gave a warning: System has non-zero total charge: -6 ( i have six peptides)

Re: [gmx-users] R: Re: rhombic dodecahedron and g_sas

Hi Anna, That was indeed the sort of output I meant; just what g_sas is blurting to the screen :) Now it completely eludes me why non-rectangular boxes might give wrong results. The code doesn't help much either. But if you want to be sure that your results are good, you can first make the molecu

Re: [gmx-users] reg explicit and implicit solvent model

vidhya sankar wrote: Dear justin, Thank you for your previous reply what is explicit and implicit solvent model ? Please use Google and/or your favorite simulation textbook. In gromacs Normally which one is implemented and used bydefault There is n

Re: Res: [gmx-users] Topology for nBuOH

Juliana Angeiras wrote: Hi, really the problem was with the order, but now i have another problem (below). I have already read the chapter 5, but i didn't fix my problem. I would like to use an archive .itp for the butanol, although i use the tip3p for water in the system (mixture water-bu

[gmx-users] R: Re: rhombic dodecahedron and g_sas

Dear Tsjerk, thank you very much for your answer. What do you mean saying that I should have provided "the exact output of g_sas"? Do you mean that I have to send you the resulting .xvg file? If you are meaning the exact words that appear on the screen when I launch g_sas, they are exactly what I w

Re: [gmx-users] Residence time and trjorder

Mark is right g_dist can help you for this but there is no specific tool calculating residence time ... I guess everyone dreams of someone writing it :)) On Jul 13, 2011, at 2:28 AM, Mark Abraham wrote: On 13/07/2011 5:52 PM, Carla Jamous wrote: Dear Xavier, my problem is the following: I'

[gmx-users] reg explicit and implicit solvent model

Dear justin, Thank you for your previous reply   what is explicit and implicit solvent model ?   In gromacs  Normally which one is implemented and used bydefault I want to use explicit solvent model in order to account electrostatic effect of ions  on H-bondi

Res: [gmx-users] Topology for nBuOH

Hi, really the problem was with the order, but now i have another problem (below). I have already read the chapter 5, but i didn't fix my problem. I would like to use an archive .itp for the butanol, although i use the tip3p for water in the system (mixture water-butanol), I want use different

Re: [gmx-users] extending PMF

Rebeca García Fandiño wrote: Hello, I am trying to extend a PMF calculation (Umbrella Sampling calculation). In first place I used tpbconv: tpbconv -s umbrella_3.tpr -o umbrella_3b.tpr -extend 1000 And then I run it using mdrun: mdrun -s umbrella_3b.tpr -cpi umbrella_3.cpt -pf pullf-umbrel

[gmx-users] extending PMF

Hello, I am trying to extend a PMF calculation (Umbrella Sampling calculation). In first place I used tpbconv: tpbconv -s umbrella_3.tpr -o umbrella_3b.tpr -extend 1000 And then I run it using mdrun: mdrun -s umbrella_3b.tpr -cpi umbrella_3.cpt -pf pullf-umbrella_3.xvg -px pullx-umbrella_3.x

Re: [gmx-users] rhombic dodecahedron and g_sas

Hi Anna, It would have been best if you provided us the exact output of g_sas. In any case, the classification of your atoms has nothing to do with the type of PBC. It has to do with the fact you're using a .gro file as a reference, which contains no charges. As a consequence, all atoms are taken

[gmx-users] rhombic dodecahedron and g_sas

Dear all, once again about this subject (I'm not sure I'll do another simulation in a rhombic dodecahedron system...) I used g_sas to compute solvent accessible surface area of my system. The command was: g_sas -f prot_boxdodfull_mol.xtc -s prot_boxdodfull_molrenum.gro -o prot_boxdodfull_sas.xvg

Re: [gmx-users] Simulation runs on iMac but explodes on cluster

> > I'd still be skeptical. 15000 steps is a long time for the trajectories to > diverge. If you can run to 14550 with SSE and stop, and then show that > continuing with SSE explodes and unoptimized kernels do not, then you have > serious evidence of a bug. Diagnosing the cause of such a bug will n

Re: [gmx-users] Simulation runs on iMac but explodes on cluster

Hi Mark, Thanks for the information and help. OK, but that can be just lucky - how lucky depends on your preparation > protocol, which you haven't told us about. You are not actually doing the > same calculation on both machines - the processes are chaotic even if > everything seems equivalent. >

Re: [gmx-users] Simulation runs on iMac but explodes on cluster

On 13/07/2011 7:32 PM, Luke Goodsell wrote: Hi Per, I did as you suggested and it's just reached step 15000 and is still going. Many thanks indeed! I'd still be skeptical. 15000 steps is a long time for the trajectories to diverge. If you can run to 14550 with SSE and stop, and then show th

Re: [gmx-users] Simulation runs on iMac but explodes on cluster

Hi Per, I did as you suggested and it's just reached step 15000 and is still going. Many thanks indeed! Is there something I can do to extract useful debugging information to submit to redmine? Luke On Wed, Jul 13, 2011 at 10:00, Per Larsson wrote: > Hi! > > Could you try running with GMX_NOO

Re: [gmx-users] Simulation runs on iMac but explodes on cluster

On 13/07/2011 7:01 PM, Luke Goodsell wrote: Hi Mark, Perhaps your simulation is intrinsically unstable, and you haven't gotten unlucky enough yet on the iMac. Check out http://www.gromacs.org/Documentation/Terminology/Blowing_Up The simulation on the iMac reaches a stable equilibriu

Re: [gmx-users] Simulation runs on iMac but explodes on cluster

Hi Mark, Perhaps your simulation is intrinsically unstable, and you haven't gotten > unlucky enough yet on the iMac. Check out http://www.gromacs.org/** > Documentation/Terminology/**Blowing_Up > The simulation on the iMac reaches a sta

Re: [gmx-users] Simulation runs on iMac but explodes on cluster

Hi! Could you try running with GMX_NOOPTIMIZEDKERNELS=1, to see if this could potentially be a bug in the sse code (I noticed nb_kernel410_x86_64_sse in your error message. Thanks /Per 13 jul 2011 kl. 09.35 skrev Luke Goodsell: > As the subject suggests, I have a simulation that runs corre

Re: [gmx-users] Simulation runs on iMac but explodes on cluster

Hi Emanuel, What kind of compounds are you simulating? > > ~1800 atom protein > What size of box are you using? > Not sure of specifics, since the tpr file was provided by a collaborator, but it appears to be ~ 7nm in each dimension > > > Do you run on multiple thread when you run i

Re: [gmx-users] Residence time and trjorder

On 13/07/2011 5:52 PM, Carla Jamous wrote: Dear Xavier, my problem is the following: I'm trying to figure out if a water molecule is present in a specific area around my protein and if so, which water molecule is that and how long does it stay in that place. I think g_dist does this for a g

Re: [gmx-users] Simulation runs on iMac but explodes on cluster

On 13/07/2011 5:35 PM, Luke Goodsell wrote: Hi, As the subject suggests, I have a simulation that runs correctly on my iMac, but fails when I try to run it on a cluster, and I am hoping someone may be able to suggest which things to try first to resolve the issue. Background: The simulation

RE: [gmx-users] Simulation runs on iMac but explodes on cluster

Hi Luck, Could you give all the necessary information about your system to help us to figure where the problem could be? What kind of compounds are you simulating? What size of box are you using? Do you run on multiple thread when you run it on your iMac? How many CPU's are you using on the clu

Re: [gmx-users] Residence time and trjorder

Dear Xavier, my problem is the following: I'm trying to figure out if a water molecule is present in a specific area around my protein and if so, which water molecule is that and how long does it stay in that place. As you said, if I google residence time, here's the definition: *Residence time*

[gmx-users] Simulation runs on iMac but explodes on cluster

Hi, As the subject suggests, I have a simulation that runs correctly on my iMac, but fails when I try to run it on a cluster, and I am hoping someone may be able to suggest which things to try first to resolve the issue. Background: The simulation proceeds perfectly well on the iMac (OS X 10.5) w