[gmx-users] Fwd: How to overcome syntax errors

-- Forwarded message -- From: Seera Suryanarayana Date: Thu, May 17, 2012 at 12:07 PM Subject: How to overcome syntax errors To: jalem...@vt.edu Dear Justin, While i am running gromacs software i am getting the following syntax errors. Fatal error: Syntax error

[gmx-users] Water molecule cannot be settled

Dear Gmx Users, My system consists of a tube which is representated by atoms which are not connected via bonds. The terminals of the tube are on the edge of the box. I try to run minimization and get an error of many "water molecule cannot be settled". I observed EM with nstxout = 1 and using VMD

Re: [gmx-users] What is the autocorrelation time

16 maj 2012 kl. 23.39 skrev Christopher Neale: > Thank you Stephane. > > Unfortunately, neither of those links contains the information that I am > seeking. Those links contain some example plots of autocorrelation functions > including a discussion of time-spans over which the example time-se

Re: [gmx-users] Pressure at constant volume

17 maj 2012 kl. 05.00 skrev Juliette N.: > Hello everyone, > > I am trying to estimate the thermodynamic expression, dP/dw at > constant V and T, for my polymer-solvent system. Where P is the > pressure, w is the mass fraction, V volume and T temperature. I guess > this task can not be done by M

Re: [gmx-users] How to over come syntax errors

17 maj 2012 kl. 08.40 skrev Seera Suryanarayana: > Dear all Gromacs users, > > While i am running gromacs software i am getting the following syntax errors. > > > Fatal error: > Syntax error - File 1AX8.top, line 7934 > Last line read: > '## #include"ions.itp"' Aren't semicolons used to make

[gmx-users] parameterization of new metal ion

hello sir, thanks for your kind reply.. while setting new parameters for metal ion NI2+ i edited my ions.itp by including the following lines.. [ moleculetype ] ; molname nrexcl NI 1 [ atoms ] ; idat type res nr residu name at name cg nr charge mass 1 NI2+1

Re: [gmx-users] Fwd: How to overcome syntax errors

17 maj 2012 kl. 09.01 skrev Seera Suryanarayana: > > > -- Forwarded message -- > From: Seera Suryanarayana > Date: Thu, May 17, 2012 at 12:07 PM > Subject: How to overcome syntax errors > To: jalem...@vt.edu > > > Dear Justin, > While i am running gromacs sof

[gmx-users] Software inconsistency error with GROMACS4.5.5

Hi ALL, I am running a protein+lipid+water+ions simulation using GROAMCS4.5.5 (compiled with intel compilers on RedHat OS). The EM, NVT and few thousand steps of NPT ran fine beforw throwing up the following error: --

[gmx-users] Place water away from existing atoms

Dear Gmx users, My system consists of a tube which is representated by atoms which are not connected via bonds. genbox somehow place water molecules overlapping my tube atoms resulting in bad contacts. Is there anyway to add water e.g. 4A away from existing index file of my tube? Please, help.

Re: [gmx-users] parameterization of new metal ion

On 5/17/12 5:12 AM, priya thiyagarajan wrote: hello sir, thanks for your kind reply.. while setting new parameters for metal ion NI2+ i edited my ions.itp by including the following lines.. [ moleculetype ] ; molname nrexcl NI 1 [ atoms ] ; idat type res nr residu name at n

Re: [gmx-users] Place water away from existing atoms

genbox calculates overlaps based on vdW radii as included in vdwradii.dat in the topology folder. Increase the vdW radii of carbons to avoid water to closer that you want. Other possibilities are patiently removing undesired waters by hand after solvation or using a "ad-hoc" script. Javier E

[gmx-users] Regarding topology error.

DEar all, While i am running gromacs software i am getting following error.Let me know that error how to over come. Fatal error: Topology include file "ion.itp" not found Suryanarayana Seera, PhD student, Hyderabad, India. -- gmx-users mailing listgmx-users@gromacs.org http://lis

Re: [gmx-users] Regarding topology error.

On 5/17/12 7:05 AM, Seera Suryanarayana wrote: DEar all, While i am running gromacs software i am getting following error.Let me know that error how to over come. Fatal error: Topology include file "ion.itp" not found The name of the file is "ions.itp" not "ion.itp." -Justin

Re: [gmx-users] distance restraints

On 5/17/12 2:51 AM, Banafsheh Mehrazma wrote: Dear all I 'd like to do NOE distance restraints; according to the chapter 4 of the manual; I should specify a section for [ distance_restraints] : [ distance_restraints ] ; ai aj type index type’ low up1 up2 fac 10 16101

Re: [gmx-users] Regarding Gas Phase Torsional Energetics

Yes, you can use dihedral restraints. I performed some dihedral scans and what I did was to add an extra optimization step, after the one with restraints, with the atoms of the dihedral frozen (note that l-bfgs may not work in optimizations, I noticed that). This was to remove any side effect

Re: [gmx-users] Pressure at constant volume

On 17 May 2012 05:10, Erik Marklund wrote: > > 17 maj 2012 kl. 05.00 skrev Juliette N.: > > Hello everyone, > > I am trying to estimate the thermodynamic expression, dP/dw at > constant V and T, for my polymer-solvent system. Where P is the > pressure, w is the mass fraction, V volume and T temper

[gmx-users] Weird result of Umbrella Sampling

Dear Justin and gmx friends, Sorry to bother you again, but I am really not sure what went wrong with the umbrella sampling simulation, which I followed Justin's tutorial. The energy curve increased from zero to the maximum but suddenly went down (no plateau). I think the reason probably is my

Re: [gmx-users] Weird result of Umbrella Sampling

On 5/17/12 7:45 AM, Du Jiangfeng (BIOCH) wrote: Dear Justin and gmx friends, Sorry to bother you again, but I am really not sure what went wrong with the umbrella sampling simulation, which I followed Justin's tutorial. The energy curve increased from zero to the maximum but suddenly went down

[gmx-users] Re: Pressure at constant volume

> Hello everyone, > > I am trying to estimate the thermodynamic expression, dP/dw at > constant V and T, for my polymer-solvent system. Where P is the Hello J. - > pressure, w is the mass fraction, V volume and T temperature. I guess > this task can not be done by MD, as for constant Volume, press

Re: [gmx-users] Place water away from existing atoms

On Thu, May 17, 2012 at 11:52 AM, Javier Cerezo wrote: > genbox calculates overlaps based on vdW radii as included in vdwradii.dat > in the topology folder. Increase the vdW radii of carbons to avoid water to > closer that you want. Other possibilities are patiently removing undesired > waters b

Re: [gmx-users] Place water away from existing atoms

On 5/17/12 9:00 AM, Steven Neumann wrote: On Thu, May 17, 2012 at 11:52 AM, Javier Cerezo mailto:j...@um.es>> wrote: genbox calculates overlaps based on vdW radii as included in vdwradii.dat in the topology folder. Increase the vdW radii of carbons to avoid water to closer that y

Re: [gmx-users] Place water away from existing atoms

On Thu, May 17, 2012 at 2:06 PM, Justin A. Lemkul wrote: > > > On 5/17/12 9:00 AM, Steven Neumann wrote: > >> >> >> On Thu, May 17, 2012 at 11:52 AM, Javier Cerezo > j...@um.es>> >> >> wrote: >> >>genbox calculates overlaps based on vdW radii as included in >> vdwradii.dat in >>the topolo

Re: [gmx-users] Place water away from existing atoms

On 5/17/12 9:24 AM, Steven Neumann wrote: On Thu, May 17, 2012 at 2:06 PM, Justin A. Lemkul mailto:jalem...@vt.edu>> wrote: On 5/17/12 9:00 AM, Steven Neumann wrote: On Thu, May 17, 2012 at 11:52 AM, Javier Cerezo mailto:j...@um.es> >>

Re: [gmx-users] Place water away from existing atoms

On Thu, May 17, 2012 at 2:30 PM, Justin A. Lemkul wrote: > > > On 5/17/12 9:24 AM, Steven Neumann wrote: > >> >> >> On Thu, May 17, 2012 at 2:06 PM, Justin A. Lemkul > > wrote: >> >> >> >>On 5/17/12 9:00 AM, Steven Neumann wrote: >> >> >> >>On Thu, May 17, 2012

[gmx-users] grompp error - incorrect number of parameters

Hello After grompp -f em.mdp -p topol.top -c solvated.gro -o em.tpr I got the error: Incorrect number of parameters - found 2, expected 4 or 4 for U-B. I thought that this could be an inconsistency be declaring the functions, but in my topology I have function 4 (for improper dihedrals)

Re: [gmx-users] grompp error - incorrect number of parameters

On 5/17/12 9:47 AM, Lara Bunte wrote: Hello After grompp -f em.mdp -p topol.top -c solvated.gro -o em.tpr I got the error: Incorrect number of parameters - found 2, expected 4 or 4 for U-B. I thought that this could be an inconsistency be declaring the functions, but in my topology I

Re: [gmx-users] Place water away from existing atoms

Well, I am still getting the same error when I try to do minimization: "water molecule on atom X cannot be settled" - these water molecules are not close to the Tube surface. If I will remove them the same error will occur but on the other atoms. If I specified only vdwradii for my Tube atoms why i

Re: [gmx-users] Two [ dihedrals ] sections in topology

Hi grompp -f em.mdp -p topol.top -c solvated.gro -o em.tpr gives me errors like ERROR 1 [file topol.top, line 233]:   No default Improper Dih. types and so on. This line 233 is the starting of my empty [ dihedrals ] block. I erase it by hand out of my topology, so that only the correct [ dihed

Re: [gmx-users] Place water away from existing atoms

On 5/17/12 10:38 AM, Steven Neumann wrote: Well, I am still getting the same error when I try to do minimization: "water molecule on atom X cannot be settled" - these water molecules are not close to the Tube surface. If I will remove them the same error will occur but on the other atoms. If I

Re: [gmx-users] Two [ dihedrals ] sections in topology

On 5/17/12 10:48 AM, Lara Bunte wrote: Hi grompp -f em.mdp -p topol.top -c solvated.gro -o em.tpr gives me errors like ERROR 1 [file topol.top, line 233]: No default Improper Dih. types and so on. This line 233 is the starting of my empty [ dihedrals ] block. I erase it by hand out of m

[gmx-users] Re: mixing Urey-Bradley and armonic in the same rtp file

Dear gromacs users, I think I solved the problem. I converted armonic angle potentials in the Urey-Bradley potentials using 0 as constant for the 1-3 bond potential. Is it right in your opinion? Francesco 2012/5/16 francesco oteri > Dear gromacs users, > > I am trying to port in gromacs the C

Re: [gmx-users] Place water away from existing atoms

Thank you. Is it possible that this is caused by the trapped molecules inside my tube? My tube ends are on the box edges so water cannot migrate outside the tube where are the other water molecules. Steven On Thu, May 17, 2012 at 3:59 PM, Justin A. Lemkul wrote: > > > On 5/17/12 10:38 AM, Steve

Re: [gmx-users] Two [ dihedrals ] sections in topology

Hi Just for correct understanding: In this "empty" [ dihedrals ] bock are 11 lines without equilibrium angle and force constant, that looks like: [ dihedrals ] ;  ai    aj    ak    al funct    c0    c1    c2    c3    c4    c5     2 1    19   

Re: [gmx-users] Place water away from existing atoms

On 5/17/12 11:16 AM, Steven Neumann wrote: Thank you. Is it possible that this is caused by the trapped molecules inside my tube? My tube ends are on the box edges so water cannot migrate outside the tube where are the other water molecules. I take it that your tube is finite, not infinite?

Re: [gmx-users] Place water away from existing atoms

My tube is finite. I increased my box so the water could interact with all water molecules. The same problem: My minim.mdp ; minim.mdp - used as input into grompp to generate em.tpr ; Parameters describing what to do, when to stop and what to save integrator= steep; Algorithm (steep = stee

Re: [gmx-users] Two [ dihedrals ] sections in topology

Hi 2012/5/17 Lara Bunte > Hi > > Just for correct understanding: In this "empty" [ dihedrals ] bock are 11 > lines without equilibrium angle and force constant, that looks like: > > > [ dihedrals ] > ; aiajakal functc0c1 > c2c3c4

[gmx-users] Force Constants and Unit Systems

Hello I never had contact with such units. Could you please help me and explain me how to transform following units:   1.) kcal / mol --> kJ / (mol * nm^2) 2.) kcal / (mol * rad^2) --> kJ / (mol * rad^2) I have additionally some question to that:  Both should be units of a force constant. From

Re: [gmx-users] Place water away from existing atoms

On 5/17/12 11:50 AM, Steven Neumann wrote: My tube is finite. I increased my box so the water could interact with all water molecules. The same problem: My minim.mdp ; minim.mdp - used as input into grompp to generate em.tpr ; Parameters describing what to do, when to stop and what to save int

[gmx-users] charm in gromacs

Dear gromacs users, I am trying to port a set of charm parameter in gromacs. I am using the script convert_charmm_to_gromacs.pl contained in the file charmm_to_gromacs.tgz ( http://www.gromacs.org/@api/deki/files/76/=charmm_to_gromacs.tgz). Regarding dihedrals, the entry regarding the file says t

Re: [gmx-users] Force Constants and Unit Systems

On 5/17/12 12:25 PM, Lara Bunte wrote: Hello I never had contact with such units. Could you please help me and explain me how to transform following units: 1.) kcal / mol --> kJ / (mol * nm^2) One cannot convert between these units, since kcal/mol is an energy term, and kJ/(mol nm^2) is a

Re: [gmx-users] Force Constants and Unit Systems

Hi >One cannot convert between these units, since kcal/mol is an energy term, and >kJ/(mol nm^2) is a force constant. This confuses me, because in the paper where that constants are from is written, I quote: "Force constant k in kcal / mol calculated by DFT" In my parametrization I have th

Re: [gmx-users] Force Constants and Unit Systems

On 5/17/12 12:58 PM, Lara Bunte wrote: Hi One cannot convert between these units, since kcal/mol is an energy term, and kJ/(mol nm^2) is a force constant. This confuses me, because in the paper where that constants are from is written, I quote: "Force constant k in kcal / mol calculated

Re: [gmx-users] Force Constants and Unit Systems

Hi Lara, On Thu, 2012-05-17 at 17:58 +0100, Lara Bunte wrote: > Hi > > > >One cannot convert between these units, since kcal/mol is an energy term, and > >kJ/(mol nm^2) is a force constant. > > > This confuses me, because in the paper where that constants are from is > written, I quote: Whi

Re: [gmx-users] Force Constants and Unit Systems

Hi >Therefore either they have a potential of the form 1/[Length] or they >weren't using the term correctly. But a 1/[lenght] potential, which is a coulomb potential makes no sense for springs, that have a quadratic potential, like V(x) = 1/2 * k * x^2 of a harmonic oscillator.  So that means

Re: [gmx-users] Force Constants and Unit Systems

On 5/17/12 1:33 PM, Lara Bunte wrote: Hi Therefore either they have a potential of the form 1/[Length] or they weren't using the term correctly. But a 1/[lenght] potential, which is a coulomb potential makes no sense for springs, that have a quadratic potential, like V(x) = 1/2 * k * x^2 of

Re: [gmx-users] Force Constants and Unit Systems

Hi what I meant was, that if a force constant would have the unit kcal/mol, the corresponding potential will be a coulomb potential and I said that this makes no sense. Springs has a quadratic potential, not a Coulomb Potential, like V(r) = 1/r. Please have a look on page 45, there you can see

Re: [gmx-users] Force Constants and Unit Systems

On 5/17/12 3:32 PM, Lara Bunte wrote: Hi what I meant was, that if a force constant would have the unit kcal/mol, the corresponding potential will be a coulomb potential and I said that this makes no sense. Springs has a quadratic potential, not a Coulomb Potential, like V(r) = 1/r. Please

[gmx-users] repulsive interaction i and i+2

Hi all, I have used a user define potential to describe attractive potential beyond i and i+3 atoms(similar to lLJ). If i want to describe repulsive interactions with in i and i+3 , how can i do it in gromacs? can anyone suggest me a way, Thanks and Regards, Mohan -- gmx-users mailing

Re: [gmx-users] Place water away from existing atoms

On Thu, May 17, 2012 at 5:48 PM, Justin A. Lemkul wrote: > > > On 5/17/12 11:50 AM, Steven Neumann wrote: > >> My tube is finite. I increased my box so the water could interact with >> all water >> molecules. The same problem: My minim.mdp >> >> ; minim.mdp - used as input into grompp to generate

Re: [gmx-users] Place water away from existing atoms

On 5/17/12 4:45 PM, Steven Neumann wrote: On Thu, May 17, 2012 at 5:48 PM, Justin A. Lemkul mailto:jalem...@vt.edu>> wrote: On 5/17/12 11:50 AM, Steven Neumann wrote: My tube is finite. I increased my box so the water could interact with all water molecules. Th

[gmx-users] Atom O5' not found in residue seq.nr. 1 while adding atom

Dear Gromacs Users, I m trying to simulate a DNA structure with amber03 force field. However, when I give first command of pdb2gmx. Following error comes: Fatal error: Atom O5' not found in residue seq.nr. 1 while adding atom. As O5' is present in DA nucleic acid. So,I

Re: [gmx-users] charm in gromacs

On 18/05/2012 2:52 AM, francesco oteri wrote: Dear gromacs users, I am trying to port a set of charm parameter in gromacs. I am using the script convert_charmm_to_gromacs.pl contained in the file charmm_to_gromacs.tgz (http://www.gromacs.org/@api/deki/file

Re: [gmx-users] What is the subroutine for SHAKE or RATTLE? Thanks.

On 17/05/2012 11:48 AM, kevin wrote: Thanks. I think I should have a look at some specific documents to understand the flow of control. Namely, to understand what is purpose of the subroutines in src/mdlib/. But I could not find such information in the Gromacs user manual. Do anyone know suc

Re: [gmx-users] grompp error - incorrect number of parameters

On 17/05/2012 11:47 PM, Lara Bunte wrote: Hello After grompp -f em.mdp -p topol.top -c solvated.gro -o em.tpr I got the error: Incorrect number of parameters - found 2, expected 4 or 4 for U-B. I thought that this could be an inconsistency be declaring the functions, but in my topology

[gmx-users] Regarding errors.

Dear all, While i am running gromacs software i am getting following error.Let me know how to over come that error Fatal error: number of coordinates in coordinate file (208L_ion.gro, 62283) does not match topology (208L.top, 62293) Suryanarayana Seera, PhD student, Hyd

Re: [gmx-users] Regarding errors.

On 18/05/2012 4:43 PM, Seera Suryanarayana wrote: Dear all, While i am running gromacs software i am getting following error.Let me know how to over come that error Fatal error: number of coordinates in coordinate file (208L_ion.gro, 62283) does not match topology (20

[gmx-users] Regarding error.

Dear all, While i am running gromacs software i am getting following error.Let me know that error how to over come. Fatal error: Residue 'CSD' not found in residue topology database Suryanarayana Seera, PhD student, Hyderabad, India. -- gmx-users mailing listgmx-users@gromacs.