Re: [gmx-users] POSITION RESTRAIN ERROR

On 9/25/13 6:05 AM, MUSYOKA THOMMAS wrote: Dear Users, I am running Protein-Ligand MD simulations. Whenever, i get to do the Position restrain run of both my protein and ligand, i get this error; Making 1D domain decomposition 4 x 1 x 1 starting mdrun 'Protein in water' 5 steps,100.0 ps

[gmx-users] POSITION RESTRAIN ERROR

Dear Users, I am running Protein-Ligand MD simulations. Whenever, i get to do the Position restrain run of both my protein and ligand, i get this error; Making 1D domain decomposition 4 x 1 x 1 starting mdrun 'Protein in water' 5 steps,100.0 ps. step 0 Step 8, time 0.016 (ps) LINCS WARNING

Re: [gmx-users] position restrain dynamics error

On 5/8/13 3:07 AM, Subramaniam Boopathi wrote: Dear Sir, I am succesfully run molecules upto energy minimization, in case of position restrain md step , i have following, could you help to overcome the A charge group moved too far between two domain decomposition steps. Step 1, time 0

[gmx-users] position restrain dynamics error

Dear Sir, I am succesfully run molecules upto energy minimization, in case of position restrain md step , i have following, could you help to overcome the A charge group moved too far between two domain decomposition steps. Step 1, time 0.002 (ps) LINCS WARNING relative constraint deviati

Re: [gmx-users] position restrain of DNA

On 2/22/13 4:37 AM, Mehdi Bagherpour wrote: Tanks Justin Should I use from 'define = -DPOSRES' in mdp file? Use whatever #ifdef construct makes sense. The -DPOSRES uses the default posre.itp written by pdb2gmx, which restrains all heavy atoms. Unless you've modified the topology, that

Re: [gmx-users] position restrain of DNA

Tanks Justin Should I use from 'define = -DPOSRES' in mdp file? On Fri, Feb 22, 2013 at 4:13 AM, Justin Lemkul wrote: > > > On 2/21/13 7:35 PM, Mehdi Bagherpour wrote: > >> Thanks Justin >> >> I have any question? >> >> i will use minimization with this restrain. >> >> using genrestr I make m

Re: [gmx-users] position restrain of DNA

On 2/21/13 7:35 PM, Mehdi Bagherpour wrote: Thanks Justin I have any question? i will use minimization with this restrain. using genrestr I make min.itp. how should I use this .itp file in grompp or mdrun? As you would any other .itp file; #include it in the topology, within the corres

Re: [gmx-users] position restrain of DNA

Thanks Justin I have any question? i will use minimization with this restrain. using genrestr I make min.itp. how should I use this .itp file in grompp or mdrun? On Fri, Feb 22, 2013 at 2:41 AM, Justin Lemkul wrote: > > > On 2/21/13 6:09 PM, Mehdi Bagherpour wrote: > >> I am using Gromacs

Re: [gmx-users] position restrain of DNA

On 2/21/13 6:09 PM, Mehdi Bagherpour wrote: I am using Gromacs software for DNA simulation. Specially in my project I need to fix two ends base pairs of DNA,The DNA that I want to simulate has 12 sequence shown bellow 5-- *C*GCAACG*C* --3 3-- *G*CGTTGC*G* --5 I dont know how I can us

Re: [gmx-users] position restrain

Justin A. Lemkul wrote: parto haghighi wrote: Dear GMX users, I am working on lipid_drg system my drug molecule has 23 atoms. [ moleculetype ] ; Name nrexcl DRG 3 [ atoms ] ; nr type resnr resid atom cgnr charge mass 1 CH3 1 DRG CAA 1 -0.073

Re: [gmx-users] position restrain

parto haghighi wrote: Dear GMX users, I am working on lipid_drg system my drug molecule has 23 atoms. [ moleculetype ] ; Name nrexcl DRG 3 [ atoms ] ; nr type resnr resid atom cgnr charge mass 1 CH3 1 DRG CAA 1 -0.073 15.0350 2 CH2

[gmx-users] position restrain

Dear GMX users, I am working on lipid_drg system my drug molecule has 23 atoms. [ moleculetype ] ; Name nrexcl DRG 3 [ atoms ] ; nr type resnr resid atom cgnr charge mass 1 CH3 1 DRG CAA 1 -0.073 15.0350 2 CH2 1 DRG CAH 2

Re: [gmx-users] position restrain file

Ping wrote: Hi all, Does anyone know how to mannually make a position restrain file? There is a protein and a dendrimer in my system. And I want the protein to be the reference group. http://www.gromacs.org/Documentation/Gromacs_Utilities/genrestr -Justin Thank you in advance. Xiuping

[gmx-users] position restrain file

Hi all, Does anyone know how to mannually make a position restrain file? There is a protein and a dendrimer in my system. And I want the protein to be the reference group. Thank you in advance. Xiuping -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/g

Re: [gmx-users] Position Restrain

pandeyprithvi...@gmail.com wrote: Dear all, I am trying to put a chain of polyleucine in water - hexane interface. Now after putting the chain of the peptide there are some overlaps. To get rid of those overlaps I tried to run a MD with the position of polyleucine constant (or restrained). Bu

[gmx-users] Position Restrain

Dear all, I am trying to put a chain of polyleucine in water - hexane interface. Now after putting the chain of the peptide there are some overlaps. To get rid of those overlaps I tried to run a MD with the position of polyleucine constant (or restrained). But during energy minimization the

Re: [gmx-users] Position Restrain md

Jamie Seyed wrote: Hi Justin, Thanks for your complete answer. Actually I have another question here. It is about potential energy after mdrun. From md.log in AVERAGES section I have potential=8.81e+04 !!! and it is 9.3e+04 from em.log the same order. Can I trust these results or I did somet

Re: [gmx-users] Position Restrain md

Hi Justin, Thanks for your complete answer. Actually I have another question here. It is about potential energy after mdrun. From md.log in AVERAGES section I have potential=8.81e+04 !!! and it is 9.3e+04 from em.log the same order. Can I trust these results or I did something wrong? Is it always t

Re: [gmx-users] Position Restrain md

Jamie Seyed wrote: Hi, How can I make sure that position restraint is actually applied (after grompp & mdrun)? When I grep "POSRES" or "posres" I can not see any information... Many Thanks in Advance/Jamie If your topology has the appropriate #ifdef POSRES, and you have "define = -DPOSRE

Re: [gmx-users] Position Restrain md

Hi, How can I make sure that position restraint is actually applied (after grompp & mdrun)? When I grep "POSRES" or "posres" I can not see any information... Many Thanks in Advance/Jamie On Fri, Aug 14, 2009 at 9:07 PM, Mark Abraham wrote: > Jamie Seyed wrote: > >> Hi Mark, >> Thanks for the answ

Re: [gmx-users] Position Restrain md

Jamie Seyed wrote: Hi Mark, Thanks for the answers. One question still remains for me: in the fws tutorial for PR step it only uses the pr.mdp (define = -DPOSRES) and run grompp followed by mdrun... Am I missing some thing? Because I can not see it introduces something that to be restrained..?? W

Re: [gmx-users] Position Restrain md

Hi Mark, Thanks for the answers. One question still remains for me: in the fws tutorial for PR step it only uses the pr.mdp (define = -DPOSRES) and run grompp followed by mdrun... Am I missing some thing? Because I can not see it introduces something that to be restrained..?? Would you please let m

Re: [gmx-users] Position Restrain md

Jamie Seyed wrote: Dear all, I have questions regarding the position restrain md. I tried to find the answer of my questions from the mailing list, but it is not clear yet. In the fws tutorial when it says (in the pr.mdp) tc_grps=Protein non-protein (1) Doesn't that mean everything in the syste

[gmx-users] Position Restrain md

Dear all, I have questions regarding the position restrain md. I tried to find the answer of my questions from the mailing list, but it is not clear yet. In the fws tutorial when it says (in the pr.mdp) tc_grps=Protein non-protein (1) Doesn't that mean everything in the system? I think for this c

[gmx-users] POSITION-RESTRAIN

message -- From: Morteza Khabiri Subject: [gmx-users] POSITION-RESTRAIN To: gmx-users at gromacs.org Date: Monday, 27 July, 2009, 7:35 PM Dear gmxusers. I want to restrain the lipids in my system which contains protein,lipid and water. I make the restraint itp file by genpr then I added it in

Re: [gmx-users] POSITION-RESTRAIN

--- On Mon, 27/7/09, Morteza Khabiri wrote: From: Morteza Khabiri Subject: [gmx-users] POSITION-RESTRAIN To: gmx-users@gromacs.org Date: Monday, 27 July, 2009, 7:35 PM Dear gmxusers. I want to restrain the lipids in my system which contains protein,lipid and water. I make the restraint itp

Re: [gmx-users] POSITION-RESTRAIN

Morteza Khabiri wrote: Dear gmxusers. I want to restrain the lipids in my system which contains protein,lipid and water. I make the restraint itp file by genpr then I added it in toplogy file. After doing grompp to make tpr file I get the following message: Fatal error: [ file "posre_entirelipi

[gmx-users] POSITION-RESTRAIN

Dear gmxusers. I want to restrain the lipids in my system which contains protein,lipid and water. I make the restraint itp file by genpr then I added it in toplogy file. After doing grompp to make tpr file I get the following message: Fatal error: [ file "posre_entirelipid1.itp", line 56 ]:

Re: [gmx-users] position restrain Software inconsistency error: Some interactions seem to be assigned multiple times

Creighton Buie wrote: Hello Gromacs Community, I am trying to set up a system where there is a coarse grained hydrophobic polymer floor in a solvated water box. I am using the martini force field with an .itp file for the polymer. The "floor" is basically the polymer spaced 0.5 nm apart from

[gmx-users] position restrain Software inconsistency error: Some interactions seem to be assigned multiple times

Hello Gromacs Community, I am trying to set up a system where there is a coarse grained hydrophobic polymer floor in a solvated water box. I am using the martini force field with an .itp file for the polymer. The "floor" is basically the polymer spaced 0.5 nm apart from each other and the bott

Re: [gmx-users] position restrain

shahrbanoo karbalaee wrote: Dear justin can I use pcouple=yes in pr.mdp ?what is defferent in my data when I use pcouple=no? pcoupl = yes doesn't do anything. You have to specify the type of pressure coupling (grompp should tell you that). For a discussion of the differences of

[gmx-users] position restrain

Dear justin can I use pcouple=yes in pr.mdp ?what is defferent in my data when I use pcouple=no? best sh-karbalaee ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive a

Re: Re: [gmx-users] Position restrain of protein and membrane

Thanks Justin for your reply, You mean to say that first keep PR on protein allowing the lipids to move(packing), later switch over to production run without keep PR on lipids? Here iam getting doubt that, While embedding protein into popc some of the lipids will be deleted led to creation of

[gmx-users] Position restrain of protein and membrane

Thanks Justin for your reply, You mean to say that first keep PR on protein allowing the lipids to move(packing), later switch over to production run without keep PR on lipids? Here iam getting doubt that, While embedding protein into popc some of the lipids will be deleted led to creation o

Re: Re: [gmx-users] Position restrain of protein and membrane

Thanks Justin for your reply, You mean to say that first keep PR on protein allowing the lipids to move(packing), later switch over to production run without keep PR on lipids? Here iam getting doubt that, While embedding protein into popc some of the lipids will be deleted led to creation of

Re: [gmx-users] Position restrain of protein and membrane

minnale wrote: Thanks for reply Justin, can I do this way first I will keep PR on popc later protein, I dont want keep PR on water.Can I do like this? You could, but I don't see the point. In equilibrating membrane protein systems, it is very important to optimize the lipid positions arou

Re: Re: [gmx-users] Position restrain of protein and membrane

Thanks for reply Justin, can I do this way first I will keep PR on popc later protein, I dont want keep PR on water.Can I do like this? Thanks in advance. On Tue, 16 Sep 2008 Justin A.Lemkul wrote : > > >minnale wrote: >>Thanks Justin for your kind reply, you misunderstood my query,now I am as

Re: [gmx-users] Position restrain of protein and membrane

minnale wrote: Thanks Justin for your kind reply, you misunderstood my query,now I am asking you clearly that, while doing membrane protein equilibration steps on which system( either protein or membrane or both) I have keep to position restrain? is there any conventional way to keep restrain

Re: Re: [gmx-users] Position restrain of protein and membrane

Thanks Justin for your kind reply, you misunderstood my query,now I am asking you clearly that, while doing membrane protein equilibration steps on which system( either protein or membrane or both) I have keep to position restrain? is there any conventional way to keep restrain? or it can change

RE: [gmx-users] position restrain

Thanks for your help. My simulation ran with your idea. > Date: Thu, 15 Nov 2007 13:34:40 -0500 > From: [EMAIL PROTECTED] > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] position restrain > > If you read the documentation for g

Re: [gmx-users] position restrain

If you read the documentation for genpr, it tells you that it will only generate a position restraint file for the first molecule, so grompp is telling you that only the protein is being restrained, which is what you should expect. If you really insist on restraining the water molecules, try readi

[gmx-users] position restrain

hi I have a system of protein, popc,water and Cl ions. I want to position restrain protein and water as without position restrain water is going into the membrane . So I made a group of protein and water together using make_ndx and then genpr. When i ran grompp i got the following error:

RE: [gmx-users] Position restrain

ckholm, Sweden > > > > -Original Message- > From: [EMAIL PROTECTED] on behalf of Uwe Richter > Sent: Thu 6/1/2006 11:33 AM > To: Discussion list for GROMACS users > Subject: Re: [gmx-users] Position restrain > > Hi, > > concept of 'molecules&

RE: [gmx-users] Position restrain

Title: RE: [gmx-users] Position restrain mh, actually the status is like this: my system is made of two kind of molecules: one (solvent) with 12 atoms and the other with  more (thousands); i tried to run only with the "big" molecule and it works perfectly, it means the atoms rest

Re: [gmx-users] Position restrain

Hi, concept of 'molecules' as it is applied within Gromacs has been discussed several times already, also with regards to distance restraints, which can not be defined between different 'molecules'. Of course you can define distance restraints between 'real' molecules by having the molecules with

RE: [gmx-users] Position restrain

> While running a MD of PE with position restrain, i get this error message > > Fatal error: [ file "posre.itp", line 6 ]: > Atom index (101) in position_restraints out of bounds (1-12) > > My atom index goes up to 6000, why do I have to be in the 1-12 range? < Regards > > Alessan

Re: [gmx-users] Position restrain

Alessandro Mattozzi wrote: While running a MD of PE with position restrain, i get this error message Fatal error: [ file "posre.itp", line 6 ]: Atom index (101) in position_restraints out of bounds (1-12) My atom index goes up to 6000, why do I have to be in the 1-12 range? your mo

[gmx-users] Position restrain

Title: Position restrain While running a MD of PE with position restrain, i get this error message Fatal error: [ file "posre.itp", line 6 ]: Atom index (101) in position_restraints out of bounds (1-12) My atom index goes up to 6000, why do I have to be in the 1-12 range? Regar

Re: [gmx-users] Position restrain

Alessandro Mattozzi wrote: Hi How should my posres.itp look like? Is there any template available? Thank Regards genpr does generate position rstrains ... -- -- Xavier Periole - Ph.D. Dept. of Biophysical Chemistry / MD Group Univ. of Groningen Nijenborgh

[gmx-users] Position restrain

Title: Position restrain Hi How should my posres.itp look like? Is there any template available? Thank Regards Alessandro Mattozzi M.Phil., Ph.D. student Dept. of Fibre and Polymer Technology Royal Institute of Technology Stockholm, Sweden ___